Did the LCA Have Teeth More Like a Gorilla?

Artificial intelligence is playing a role in understanding human evolution.  From the Australian site News.com comes a story about new work in trying to understand what the last common ancestor to apes and humans might have looked like:

IT’S an image imprinted on our brains: the steady march of evolution from chimp to human. But it’s not quite right.

Monkeys don’t belong on the tree. They have tails.

Chimps, which don’t, are with Bonobos our closest living relatives. And, as such, both should be standing alongside us in the march of life.

Stretching out behind should be a gradually converging branch of earlier variations.

Ultimately, between six and eight million years ago, the branches almost certainly converge on one common ancestor.

We know almost nothing about what that was.

We have reasonably secure evidence of bipedality at around 6 million years in the form of Orrorin tugenensis from Kenya, as well as a crushed skull from Chad called Sahelanthropus that may or may not be 7 million years old, and recently, fossil footprints, purporting to show bipedal walking, from Crete have been uncovered that have been dated to around 5.7 million years ago.  Beyond that, nothing.  That is where the new AI study comes in.

The researchers used machine learning to teach an artificial intelligence to identify and classify fossilised hominid teeth dating from 25 million years ago. It then sifted through these to find patterns of development.

The study published in the science journal PaleoBios found one tantalising tip.

Our common ancestor almost certainly had gorilla-like teeth.

Now, it’s not a lot. And it certainly doesn’t say our ancestor was a gorilla.

But what it does do is add some shape and substance to this nebulous period of our human origins.

The information that is contained in the article is not nearly as cut and dried as is indicated by the news story. From the conclusion:

Given that the divergence of humans and chimpanzees occurred in the late Miocene, and that Miocene apes are much more similar to Gorilla in dental proportions, we assert that gorillas are the more appropriate extant model for the African ape LCA in terms of the relative sizes of the postcanine teeth. This similarity in dental proportions likely has implications for the interpretation of dietary adaptation and possibly phylogenetic relationships in Miocene apes, including the chimpanzee-human last common ancestor.

What this likely means is that, during the Miocene, which was the golden age of the apes, even after the divergence of Gorillas from the main line, there were extant forms that continued to have varying degrees of traits that could be associated with gorillas, presenting a classic case of collateral ancestry.  It is possible that one of the lines eventually led to chimpanzees, while another led to us.  We won't know more until we actually have some fossil remains from that missing time period. 
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Genetic Model Identifies Paranthropus boisei as Vector For Transmission of Herpes Virus

CNN (usual caveats) reports on a study that identifies Paranthropus boisei as the likely transmission vector of genital HSV-1.  From the story:

Herpes has been around a long time, to say the least.

Ancient chimpanzees genetically passed oral herpes (herpes simplex 1, or HSV-1) to the earliest humans millions of years ago when our lineage split. And we almost missed out on catching that other scourge, genital herpes (HSV-2) -- almost. Unlike HSV-1, HSV-2 didn't make the leap to early humans on its own.

Unfortunately for modern humans, millions of years ago, an early human ancestor was in the right place at the right time to catch HSV-2. And it might not have happened if it weren't for that meddling hominin species Paranthropus boisei, according to a new study in the journal Virus Evolution.

Why Paranthropus boisei, you ask? After all, P. boisei was not even on the main line of human evolution, coexisting with all manner of early Homo species at the same time, who likely out-competed them into extinction.  From the article, which is highly technical:

Paranthropus boisei would have been well placed to act as an intermediate host for HSV2. It most likely contracted the infection through hunting or more likely scavenging infected ancestral-chimpanzee meat. Processing (with or without tools) and consumption of raw meat would act as a simple path for ChHV1 to have crossed into P.boisei via open cuts or sores. Tropical refugia during hot dry periods may have driven chimpanzees into higher concentrations in certain areas, driving them into contact and competition with P.boisei and H.habilis as the margins of tropical forest blended into more open savannah-like habitats (Julier et al. 2017). Violent confrontation or hunting/scavenging and butchery practices would have provided a viable path of transmission for HSV2. Homo habilis remains have been recovered from the same layers as stone tools and bones carrying evidence of butchery, supporting a possible transmission–through-hunting/scavenging hypothesis for the initial anc-chimp to H.habilis transmission (Clarke 2012). Paranthropus aethiopicus, P. boisei, and P. robustus are associated with the Oldowan stone tool complex (De Heinzelin et al. 1999), and P.boisei explicitly with butchery (Domínguez-Rodrigo et al. 2013) lending support to the hypothesis that bushmeat hunting/scavenging and butchery may have led to the initial transmission of HSV2 to the hominins.

The entire exercise is very mathematical and relies on somewhat limited evidence of P. boisei behavior. It is, nonetheless, intriguing since it posits considerable interaction between the various hominin groups. 

Here is a mugshot of one of the perpetrators, the Zinj skull from Olduvai Gorge, found in 1959. 

For the Want of a Chromosome Pair

Slate has an article on how we ended up with 46 chromosomes. Despite the colloquial writing style, there is some good information about how we got one less set of chromosomes than Chimpanzees, our closest relatives. Sam Kean writes:

Around a million years ago, in some fateful man or woman in Africa, what were the 12th and 13th human chromosomes (and still are the 12th and 13th chromosomes in many primates) got entangled at their tips. Instead of separating cleanly, 12 and 13 fused together, like one belt buckled onto another. This amalgam eventually became human chromosome 2.

Fusions like this are not uncommon—one in every 1,000 babies has some sort of chromosomal fusion—and most go unnoticed because they don’t upset anyone’s health. (The ends of chromosomes contain few genes, so often nothing gets disrupted.) However, a fusion by itself can’t explain the drop from 48 to 46. A fusion leaves a person with 47 chromosomes, not 46, and the odds of two identical fusions in the same cell are remote. And even after the drop to 47, the person still has to reproduce to pass on the trait, a serious barrier.

He would have to find a person also with 47 chromosomes and, despite the possibility of many miscarriages, one in thirty-six would inherit both fused chromosomes and have 46. This must have had some sort of selective advantage because that is the form in which we find ourselves today. It has been suggested that there was a genetic bottleneck (Venema also writes about this) and it is possible that this was the point that the 46 variant took over. it is thought-provoking, if speculative. One thing is certain: we have fewer chromosomes than chimpanzees and it is because of a chromosomal fusion. The key here is that we and chimpanzees share a last common ancestor.

The Diet of Australopithecus sediba

There is some suspicion that Australopithecus sediba, discovered by Lee Berger (or, rather, his son) may be on the line that eventually leads to Homo. This is not clear but right now, it is as good as any model we have. We now know a bit more about what Au. sediba ate. According to Science Daily:

Australopithecus sediba, believed to be an early relative of modern-day humans, enjoyed a diet of leaves, fruits, nuts, and bark, which meant they probably lived in a more wooded environment than is generally thought, a surprising find published in the current issue of Nature magazine by an international team of researchers that includes a Texas A&M University anthropologist.¹

The goofy thing is that these hominins (or at least the ones we have) ate much more of these kinds of items than any other hominin we have discovered. In fact, their diet is much more like that of a chimpanzee than a hominin. This probably means nothing more than that is what they had access to but it does mean they were having a diet different from the robusts. Au. sediba’s teeth are gracile, in comparison to those of the robusts or earlier australopiths. It was definitely a forested environment.

¹Amanda G. Henry, Peter S. Ungar, Benjamin H. Passey, Matt Sponheimer, Lloyd Rossouw, Marion Bamford, Paul Sandberg, Darryl J. de Ruiter, Lee Berger. The diet of Australopithecus sediba. Nature, 2012;
DOI: http://dx.doi.org/10.1038/nature11185

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Bonobo DNA Sequenced

The Los Angeles Times is reporting on a story from Nature in which the complete genome sequence of the Bonobo or Pygmy Chimpanzee, has been sequenced. Eryn Brown writes:

“There's a common ancestor that we and these apes were derived from. We want to know what that ancestor looked like,” said Wes Warren, a geneticist at Washington University in St. Louis, who was not involved in the research. “By adding the bonobo to the mix, we have a better idea.”

Now, with all the great ape sequences complete, scientists can better use genetics to help determine whether a particular trait cropped up for the first time in humans, said Kay Pruefer, a postdoctoral researcher at the Max Planck Institute in Leipzig, Germany.

Bonobos and Chimpanzees separated around 1 million years ago and are now very different behaviorally.

As an aside, much whooping and howling occurred when this story first appeared this morning. The headline now reads “Scientists map genome of the bonobo, a key human relative.” When it first came out, it read “Scientists map genome of the bonobo, a key human ancestor.” The comments were swift and brutal. Many accused the writer, Eryn Brown, of not knowing anything about science. What most don't realize is that the article is often written without the headline, which is then put in by an editor. In this case, it is likely the editor who didn't know, not the author.

It was also a tad heart-warming to see so many of the readers actually knew the correct relationship between humans and bonobos.

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Gorilla DNA Sequenced

According to a story out of the LA Times, the gorilla genome has been completely sequenced. Eryn Brown writes:

By comparing the new gorilla DNA sequence with reference genomes of humans, chimpanzees, orangutans and macaques, scientists have already made a few surprising insights into the crucial periods when we diverged into separate species.

For instance, the new genetic data bolster fossil evidence that gorillas split off as a separate species about 10 million years ago and that humans and chimps parted ways about 6 million years ago. Previous genetic evidence had seemed to point to a more recent split, prompting a contentious debate between genetics experts and fossil scholars, said Durbin, who leads the genome informatics group at the Wellcome Trust Sanger Institute in Hinxton, England.

This is good because it means that the last common ancestor can be as far back as six to seven million. Does this make Sahelanthropus or Orrorin hominins? Not necessarily but now it is a more easily acceptable position..

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Did Australopithecines Have Bonding Patterns Like Modern Chimpanzees?

The Guardian has a story on research done with Australopithecus africanus and A. robustus teeth that suggests that, while the men did not wander far from their birth site, the women did. Ian Sample writes:

“Here we have the first direct glimpse of the geographic movements of early hominids, and it appears the females preferentially moved away from their residential groups,” said lead author, Sandi Copeland at the Max Planck Institute for Evolutionary Anthropology in Leipzig.

A similar situation is seen among modern chimpanzees, where females tend to move out of their groups, in part because males form strong ties that help them protect a troop's territory.

“By virtue of the fact that the males choose to remain, the females are indirectly forced to leave their communities in order to avoid close inbreeding. It could be that among these early hominins, female dispersal has some correlation to close cooperative behaviour between males,” Copeland added.

Another piece of the puzzle.

Gibbons and Siamangs Booted off the Island

Science Daily has a story about a new Primate phylogenetic tree that has been derived from sequencing 54 genetic regions in 186 species. Over the course of the last twenty years or so, with the advent of the genetic revolution, there has been a wave of new information about the higher apes that has allowed us to break them out of their “grade” of higher apes and place them more accurately taxonomically.


It now appears that gibbons and siamangs (Hylobates, Nomascus and Symphalangus) are monophyletic with respect to the clade that includes gorillas, chimpanzees, orangs and us. I have reproduced the relevant part of the image in the PLoS article to the left. About them, the authors of the article write:

The eight species included in this study form three clades that coincide with genus designation (absent is Hoolock; nodes 64–69) that diverged rapidly 8.9 MYA. Moreover, Nomascus species appear more recent than Symphalangus and Hylobates, with node divergence dates estimated at less than 1 MY (Table 3, Table S9, Figure 2). Thus, Hylobatidae exhibits episodes of rapid divergence perhaps related to excessive genome re-organization and warrants additional investigation.

Another piece of the puzzle.

Hat Tip to Bill Myers.

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More on the Human-Orang Connexion

Here is a much longer article from Eurekalert! on the idea that humans are more closely related to orang-utans than to chimpanzees. They write:

Jeffrey H. Schwartz, professor of anthropology in Pitt's School of Arts and Sciences and president of the World Academy of Art and Science, and John Grehan, director of science at the Buffalo Museum, conducted a detailed analysis of the physical features of living and fossil apes that suggested humans, orangutans, and early apes belong to a group separate from chimpanzees and gorillas. They then constructed a scenario for how the human-orangutan common ancestor migrated between Southeast Asia—where modern orangutans are from—and other parts of the world and evolved into now-extinct apes and early humans. The study provides further evidence of the human-orangutan connection that Schwartz first proposed in his book The Red Ape: Orangutans and Human Origins, Revised and Updated (Westview Press, 2005).

Schwartz and Grehan scrutinized the hundreds of physical characteristics often cited as evidence of evolutionary relationships among humans and other great apes—chimps, gorillas, and orangutans—and selected 63 that could be verified as unique within this group (i.e., they do not appear in other primates). Of these features, the analysis found that humans shared 28 unique physical characteristics with orangutans, compared to only two features with chimpanzees, seven with gorillas, and seven with all three apes (chimpanzees, gorillas, and orangutans). Gorillas and chimpanzees shared 11 unique characteristics.

Schwartz and Grehan then examined 56 features uniquely shared among modern humans, fossil hominids—ancestral humans such as Australopithecus—and fossil apes. They found that orangutans shared eight features with early humans and Australopithecus and seven with Australopithecus alone. The occurrence of orangutan features in Australopithecus contradicts the expectation generated by DNA analysis that ancestral humans should have chimpanzee similarities, Schwartz and Grehan write. Chimpanzees and gorillas were found to share only those features found in all great apes.

Schwartz and Grehan pooled humans, orangutans, and the fossil apes into a new group called "dental hominoids," named for their similarly thick-enameled teeth. They labeled chimpanzees and gorillas as African apes and wrote in Biogeography that although they are a sister group of dental hominoids, "the African apes are not only less closely related to humans than are orangutans, but also less closely related to humans than are many" fossil apes.

As they, themselves acknowledge, the earliest hominid material is in Africa, which is where chimpanzees are and where orangs are not. They suggest that there was a migration between 12-13 mya of hominoids between east Asia and Africa before there was a separation of the different groups that eventually became chimpanzees and orang-utans. Peter Andrews seems to like the idea. I wonder how many others will sign on?

Orangs Our Closest Ancestors?

There is a short story out of the Pittsburgh Post-Gazette that Jeffrey Schwartz and John Grehan have discovered that chimpanzees may not be our closest relative but that, rather, it is the orang. The article is short but has this to say:

They conducted a detailed analysis of the physical features of living and fossil apes that suggested humans, orangutans, and early apes belong to a group separate from chimpanzees and gorillas.

According to a news release, the researchers reject as "problematic" the popular suggestion, based on DNA analysis, that humans are most closely related to chimpanzees, "which they maintain is not supported by fossil evidence."

I am guessing this will make some very large waves.