Deep Ancestry: Our Story

Anyone who is interested in family history, or anyone who has ever gone to a library or archive to undertake genealogical research knows that while the subject is an exciting one, the work can be tedious and the resulting picture often fuzzy.

This is where we stand with regards to family research writ large, that of modern humanity. To be sure, we have come a long way since we humans even became aware of the fact that we had a very long history, or a deep ancestry. Consider the day, now more than 180 years ago, when people went into a cave in Belgium and encountered remains later identified as belonging to a Neanderthal individual. Compare that against our current understanding of human evolution. How we got here is an interesting story and it is an interesting tale to relate,. Where we go from here is equally intriguing.

Here is part one: how did we get here?

Traditionally, we rely on three main sources of information when studying human origins, our origins. These sources are: the material remains of that past (including both fossil remains and man-made tools), genetics and comparative primatology. The latter refers to observation of current non-human primates and possible correlations between their habitat and behavior with the environment in which our ancestors once lived and their behavior. If there is one constant in the picture generated by these sources is that it is always being refined and updated. Such is the nature of scientific endeavor: it never stands still. Thankfully, our thirst for greater understanding is never slaked either. There is always more to investigate.

Material remains have been the backbone of paleoanthropological studies. After all, what could be a better illustration of human evolution than a fossil of an ancient ancestor, or a tool made by a distant relative of ours? By carefully plotting where these remains have been found, we can reconstruct a picture of human evolution, we can start to see where our earliest ancestors once arose, evolved and eventually migrated from. By studying their tools, we can see human inventiveness at work. At first this is a tediously slow process, but eventually we see it picking up pace to the point we are today: new gadgets developed on a daily basis.

For a while, as people were studying fossil human remains, others were investigating genetics. However, initially the practitioners of these two pursuits did not know of each other’s work, or, did not realize how their work could benefit from the other person’s insights. And so we see how Mendel and Darwin were contemporaries, but their respective scientific insights and breakthroughs did not cross over and inspire the other.

DNA rendering
Creative Commons License photo credit: ynse

Our genetic makeup is the result of millions of years of evolution.

Since the Human Genome Project was completed in 2003, we have learned a lot about our genetic makeup. Since then, the chimp genome, gorilla genome, and the orangutan genome have been finished; by the way, the latter was sequenced in our own backyard here in Houston. This provides a nice platform to start comparing our genetic makeup with that of our close primate relatives, and find out where we differ, and, more interestingly, how similar we are below the surface. It turns out we are quite similar.

The difference 1% makes.

Differences, no matter how ostensibly small, remain important. One can be in awe about the fact that we share around 99% of genes with chimps. One could also turn that around and say “See how much difference 1% makes?” That difference, in turn, may help us figure out when in time we started to go our own way, after the split from a common ancestor. This is where the notion of a molecular clock comes in. This concept has been used to “to investigate several important issues, including the origin of modern humans, the date of the human/chimpanzee divergence, and the date of the Cambrian explosion.”

Thus we see in the literature that orangutans, with whom we share around 97 % of our DNA, split from the family tree around 16 to 15 million years ago. Humans and chimps became their own branches on the family tree around 6 to 5 million years ago.

As one researcher recently put it: “There remain signals of the distant past in DNA, and our approach is to use such signals to study the genetics of our ancestors.”

The concept of the molecular clock continues to be refined as our understanding of its potential and limitations has grown. For better or worse, however, it provides us with a tool to help situate major branching events on the family tree. This brings us to our own immediate past, our place in history, when modern humans appeared on the scene.

Modern Humans

Discoveries made in East Africa date the emergence of modern human beings to about 200,000 years ago. Two skulls, found in 1967 in Ethiopia were recently identified as the earliest known modern humans. While that makes all of us Africans, it data from mitochondrial DNA have suggested that our ancestors did not make it out of Africa until 60,000 years ago. The archaeological record seems to disagree, however. Man-made tools twice that age have recently been found in the Arabian Peninsula.

It is at times like these, when dates provided by genetics and archaeology diverge, that we hear voices criticizing the invalidity of this approach. What we will see happen, however, is that this apparent disjunction between two sets of data, will spur on researchers to find where the source of this disparity lies and resolve it. Were that to be impossible then we would have to go back to the drawing board and rethink our ideas about human evolution and the timing of critical events related to it.

Now for part two: where do we go from here?

As people become more mobile, we are now finding our mates much further away than we did just a few generations ago. This means that it will become more difficult to check that box on the census form asking for our ethnicity. It also means that we are slowly becoming more homogenized. Indigenous cultures are disappearing and language follow suit.

To get an idea of how exhilarating and mind-boggling this pursuit of science can be, I would like to invite the reader to attend an upcoming lecture.

On March 7, the Houston Museum of Natural Science will host Dr. Spencer Wells, lead scientist of the Genographic Project.

His lecture, entitled “Deep Ancestry: Inside the Genomic Project,” is brought to us by the Leakey Foundation. Dr. Wells is an Explorer-in-Residence at the National Geographic Society and Frank H. T. Rhodes Class of 1956 Professor at Cornell University. Dr. Wells will share with us how the Genographic Project, using data from hundreds of thousands of people, including members of the general public, the Genographic Project is deciphering the migratory routes followed by early humans as they populated the Earth.

I look forward to this lecture, and hope to see many of you at the museum that evening.

In the meantime, a pop quiz.

Q: What do the following individuals have in common?

Brazilian indian chiefs, Kaiapos tribe, during a collective interview.
Left to right: Raony (state of Mato Grosso), Kaye, Kadjor, Panara (Pará)
Creative Commons License photo credit: Valter Campanato, Agência Brasil (ABr). April 17, 2005
Ethiopian Orthodox Christian woman – Lalibela, Ethiopia
Creative Commons License photo credit: Dirk Van Tuerenhout
Lake Titicaca – Uros people
Creative Commons License photo credit: Dirk Van Tuerenhout

A: They are us. We are them. This is us.

Your questions, answered: Do we know when chimaeras shifted to deep-water habitats?

Earlier this month we received a question on one of our past posts, The Ghost Sharks of the Jurassic, asking:

“Do we know when these chimaeras shifted to deep-water habitats? If predation and, in particular, the evolution and diversification of predatory species prompted their geographic transition, at what point would a sort of critical level have been reached to drive them into the deep? How many predators are too many?”

Why do “living fossils of the deep sea” so often represent lingering survivors of groups that long ago flourished in shallow water?


Examples: Rabbitfish (aka chimaeras), Coelacanths, Goblin Sharks, Giant Squid.

Excellent question – one that keeps evolutionary biologists awake at 2 a.m.

First thing: we never know when a clan of species invades deep water. This is why:

Sediments deposited on top of oceanic crust in deep-water – thousands of feet deep – rarely come to the surface where the layers can be seen by fossil-hunting paleontologists. Mud does form at the bottom of deep seas and fossils do form here. But such deep specimens have a low chance of being found by us.

Deep sea bottom mud is raised above sea level when continents collide and abyssal sediment is squeezed up and thrust across slabs of continental crust. There are narrow zones of such squeezed sediments – for example, in the Taconic Mountains of New York State. Here are slices of deep crust and sediment with deep-water trilobites. However, very few vertebrate and squid fossils are known from squeezed deposits.

Medium-deep sediment, up to 200 meters deep,  do form in the bottom of “epi-continental seas” like the famous  “Cretaceous Ocean of Kansas” that covered much of the central areas of North America. Such epi-continental seas  do drain away, and the bottom sediment becomes lifted hundreds or thousands of feet, so wind and water can erode valleys into the rock layers, exposing fossils. Epi-continental sea bottoms have given us 90% of our marine vertebrate and cephalopod fossils.

Coelacanth fossils are common in shallow-water and medium-deep sediments beginning in the Early Devonian, over 400 million years ago. From then on, coelacanths remain widespread and often common. Were they in deep water too? We don’t know – we don’t have enough deep sediment exposed for study.

Abruptly, coelacanths disappear from epi-continental sea deposits in the Late Cretaceous. Naturally, we thought they were extinct. But then the fish show up alive and well, hanging around at 130 meters to 700 meters.

Ditto for the Goblin Shark: common as a fossil along New Jersey in shallow sediment but now restricted to much deeper waters. Ditto for the giant squid, who left their shells in the Cretaceous epi-continental sea sediment but now prefer deeper water.

Goblin Shark

Is there a common explanation for all the survivors in deep waters?

The most popular theory is: 1) Most new types of fish and cephalopods first evolve in shallow water. 2) It takes time for evolution to modify a fish or cephalopod so the beast can survive at 200m + depths. So the early coelacanths couldn’t colonize the great depths for tens of millions of years. As more and more clans of fish evolved in shallow water, some began their adaptive descent too – but the coelacanth had a head start. Being fully adapted to great depth already may have protected the fish from predators and competitors who are behind in the degree of their transition.

There are holes in the theory. Coelacanths do have predators – they show up in shark stomachs. They must have competitors too – teleost fish with more complex jaws.

Deep Sea Refuges continue to irritate our neat little hypotheses.

WAnt more? See the past post on ghost sharks and full comment.

Human Evolution: The Year 2010 in Review (Part 2)

Make sure you check out part one of my blog, published two weeks ago.

Teeth came up in another story in 2010. Researchers were quoted as saying that modern humans, traditionally thought to have evolved roughly 200,000 years ago in East Africa, now might be 400,000 years old. In addition, they may have evolved in Israel rather than Africa. Twice as old and not from Africa, was the message spread by the media. The evidence? A few teeth found in Qesem Cave.

However, a word of caution is in order here. What was reported in the media was not what the scientists had said. In fact, they had implored the members of the press not to engage in hyperbole and present hypotheticals as proven facts. They were ignored. Someone called the media on this and chastised them for engaging in “science by press release.”

DNA made the headlines several times this past year.  In August scientists announced that they had decoded famous ice man Oetzi’s genome. This is interesting in itself; it would be even more interesting if we could compare his genetic makeup with the genome of the Tarim Basin mummies.  Such a genome has not been decoded yet, so we will have to wait. Imagine, however, the potential such a comparison would present to evaluate the origins of these Caucasoid mummies.

Oetzi the Iceman: as exhibited in Museum Bélesta (Ariège), France;
reconstruction of his equipment. Photo by: Gerbil

What lessons can we draw from all this?

First, it seems that a lot of trailblazing research is now based on minute amounts of evidence, a finger bone here, and a few teeth there.

Second, the fact that we are dealing with minute amounts of information does not detract from the importance of the scientific contributions these data have made.

Third, some of the data are microscopically small. Size notwithstanding, DNA and DNA analysis have become a very valuable component in retracing human origins.

I would like to end with an observation and a comment.

In March 2010, the Smithsonian’s National Museum of Natural History proudly opened its doors on the completely renovated David H. Koch Hall of Human Origins. It is a wonderful exhibit, sharing with millions of visitors the scientific basis of our understanding of human evolution.

On display for the first three months were three original fossils, one Cro-Magnon and two Neanderthals. Their presence was announced with great pride in the original press release.  A review by a leading US newspaper stated:  “Because of the fragility of human remains, only a handful of actual fossils are on display, diminishing the sense of wonder the real thing always inspires.”

Interestingly, the reference to the original fossils was missing in other (presumably later) online versions of that same announcement. Instead, we only find a reference to “a display of more than 75 skulls (exact replicas).”

Here is a photograph as it appeared in the media (AP Photo/Jacquelyn Martin), showcasing two of the three original skulls on display.

Treasured Neanderthal and Original Cro-Magnon
Creative Commons License photo credit: Ryan Somma

The caption read :
“Fossil skulls of La Ferrassie Neanderthal, left, and Cro-Magnon, that are on a three-month loan from the Musée de l’Homme in France, are seen in the David H. Koch Hall of Human Origins exhibit at the Smithsonian’s National Museum of Natural History in Washington. Scientists think DNA analysis of Siberian genetic material may have revealed yet another branch of the human tree.”

In an age where the human attention span seems to be measured in minutes, let alone days or even years, it is good to remember that in 2007, there was another original fossil on display in the US. The venue was the Houston Museum of Natural Science. The original fossil involved was that of Lucy.

In a very savvy media campaign, several leading paleoanthropologists engaged in variations of an ad hominem attack, and used rather unfortunate language to refer to the museum, as well as the curator of the exhibit.

The scientists who opposed Lucy going on display all invoked the same document, a 1998 statement drafted by the International Association for the Study of Human Paleontology. The second resolution in this document declares:

“We strongly recommend that original hominid fossils should not be transported beyond the country of origin unless there are compelling scientific reasons which must include the demonstration that the proposed investigations cannot proceed in the foreseeable future in the country of origin.”

Less than three years after invoking this document, the National Museum of Natural History now finds itself doing the very same thing it once so vehemently opposed. Moreover, an internet search in the days following the opening of the new hall in Washington failed to identify any criticism by the same individuals who in the previous case had brought out the big guns. As the first anniversary of the hall is just around the corner, still not a word of criticism has been uttered.

As someone once said: “Isn’t that special?”

Human evolution: the year 2010 in review (Part 1)

That’s some good-looking gombo, cher!

Creative Commons License photo credit: Southern Foodways Alliance

This blog contribution aims to be like a good Louisiana seafood gumbo: thick, hearty, spicy, and made up all kinds of finger-licking ingredients (pun intended). There will be some French, which would be apropos, some Latin as well, and all kinds of discoveries related to human origins, as they transpired this past year. I will follow up with a second part in a week or two with an observation and a comment.

In an earlier blog, “A pinky’s promise,” I wrote about the incredible discovery that was made early in 2010 when DNA analysis was performed on one small finger bone retrieved from a cave in Southern Siberia. The bone dated to a period (50,000 to 30,000 years ago) when all scientists assumed that the only living humans were either Homo sapiens sapiens or Neanderthals (perhaps we should now be saying Homo sapiens neanderthalensis, but I am getting ahead of the game). This first assumption proved to be wrong.

Entrance to the Denisova Cave
Creative Commons License photo credit:ЧуваевНиколай

In 2008, DNA analysis carried out on a single finger bone revealed that there was a third species of human walking the earth at that time. Toward the end of 2010, this view was corroborated by additional DNA analysis of a few teeth that were found in the same Denisova cave. The Max Planck Institute in Leipzig announced that these so-called “Denisovans” represent a new species.
More interesting still, some of their DNA is still around: the “Denisovans” interbred with the ancestors of Melanesians. This implies that at one point, this third species was quite widespread in Asia. If these conclusions hold up, the lesson we should take away from this breakthrough is that every little scrap of evidence counts when studying human origins, even a single tooth, or a finger bone. I wonder how many single finger bones or teeth have been overlooked in the past, or are still awaiting re-discovery in a museum drawer somewhere.

Neanderthals were also in the news this past year. For years, researchers have been vexed by questions such as “Who were these people?”, “Where did they come from?”, “What made them extinct?” and last but not least “Is there a little bit of Neanderthal in (some of) us?”

With regard to the last question, also discussed in earlier blogs, the way in which we answer that question will result in a different scientific (read: Latin) nomenclature for Neanderthal. Allow for the possibility of interbreeding between Homo sapiens and Neanderthals and also agree that their offspring was fertile, i.e., they successfully reproduced, then you would have to refer to Neanderthals as Homo sapiens neanderthalensis. If you disagree with this idea, and think it was unlikely these two populations interbred, or that their offspring was not capable of producing fertile offspring, then you would have to refer to Neanderthals as Homo neanderthalensis. This classifies them as a species separate from modern humans; by definition, species cannot interbreed and produce fertile offspring.

A Happy Neanderthal
Creative Commons License photo credit: erix!

The latter way of thinking was long popular among paleoanthropologists. Now the pendulum is swinging the other way. Scientists at the institute decoded the Neanderthal genome and compared it with that of modern humans. The result? In their words: “By comparing that genome with those of various present day humans, the team concluded that about 1 percent to 4 percent of the genome of non-Africans today is derived from Neanderthals.”  In people speak: up to 4% of a European’s genetic makeup could be inherited from the Neanderthal lineage, now extinct.

Before you check for hair on your knuckles, thank (or blame) a single finger bone and a few teeth, as well as the staff at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany for all this.

Lest we all (well, at least those of us of European descent) break out in hives and run for the nearest hills, scientists were quick to add: “[T]he Neanderthal DNA does not seem to have played a great role in human evolution.”

Certainly, 1 to 4% overlap in genetic makeup is not very much, but it is a whole lot more than we were willing to consider just a year ago. Differences between Homo sapiens sapiens and Homo sapiens neanderthalensis remain significant. The overall physical appearance of a modern human is very different from that of a Neanderthal. In terms of behavior, and cognitive abilities, the two subspecies also appear to be a world apart, never mind they shared portions of our planet.

Comparing Neanderthals and modern humans
One of the areas in which there were both similarities and differences was diet. These insights also came out this past year.  Did you know that Neanderthals ate their veggies? And that they liked to cook them as well? Perhaps you did. However, did you also know that they were not averse from eating each other?

Check back next week to see more on this, when Dirk discusses teeth, DNA, and his own conclusions to 2010 in review.