Tuesday, September 2, 2014

The Genome and Body

Our Neanderthal Inheritance

The family tree of the four groups of Hominins living in Eurasia around 50 kya, and the lingering genetic heritage due to interbreeding

Svante Paabo

The Neanderthal genome contains many secrets: their genealogy, muscle development, digestive system, diseases they carried, and their immunology. All of these aspects of Neanderthal lives were invisible from the study of their bones. As it turns out, 97% of our DNA is from Homo Sapiens, the other 3% is from Neanderthals. “Think about it in terms of numbers, today there are about 6 billion people living in the world outside of sub-Saharan Africa, 3% of their ancestry traces to Neanderthals, we're talking around about 200 million Neanderthals. Neanderthals today are more successful than they ever were when they actually existed.” -John Hawks. The 3% figure is actually an average, Neanderthal inheritance varies dramatically between human populations. Humans whose ancestors lived in paleolithic Europe and Asia are much more related to Neanderthals (up to 5%) than humans whose paleolithic ancestors lived in sub-Saharan Africa or the Americas (down to 1%). While this average may vary, all humans share some amount of Neanderthal genes. Specifically we share nuclear DNA but not mitochondrial (maternally transmitted) DNA. This prompts the hypothesis that female humans and male Neanderthals produced offspring, but male humans and female Neanderthals were either rare, absent, or sterile. The simple acknowledgment that our DNA is not wholly resultant from other Homo Sapiens shows that we, as a species, had no scruples interbreeding with other hominins. It is also solid evidence that we interbred with Neanderthals at all, which was heavily in dispute until these findings. While we obtained genes from Neanderthals, these studies also show us which genes are owned solely by ourselves, and no one else.

The most ridiculous picture of John Hawks I could find on the internet

The most important genes we inherited deal with the HLA (human leukocyte antigen) system. These HLA genes are fundamental to creating our immune system and vital to fighting off disease. Through inheritance, we adopted these genes which developed specifically within the Neanderthal immune system. Their immune system had evolved to fight off ice age diseases, which we (as recent transplants from Africa) had no immunity to. This environmental upgrade was first developed within the human population by Neanderthal and Human hybrids. These hybrids had quite the advantage of those without this enhanced immune system, enough of an advantage to slowly bring these genes back into the human population...and spread them across the world.

In a 2014 study by Liran Carmel and Eran Meshorer, which reconstructed the Neanderthal and Denisovan epigenome, researchers found human-unique genes involved with brain development (which makes sense), but also with our immune and cardiovascular systems. They discovered certain genes, like those related to our digestive system, which were shared in common with Neanderthals and humans. A 2010 study led by Liran Carmel found genes related to Alzheimer's, autism, and schizophrenia which had been (through epigenetic markers) “turned off” for Neanderthals and “turned on” for humans. This might mean that Neanderthals and humans did not share these mental illnesses, but that they are a human phenomenon. While this may be the case, epigenetic markers vary wildly between populations due to climate, diet, and a range of other factors. This individual Neanderthal did not suffer from these illnesses, it may not be emblematic of the population at large.

In a separate 2014 study by Sriram Sankararaman and David Reich, they found that we inherited Neanderthal genes related to the susceptibility for Crohn's Disease, Lupus, and Type 2 Diabetes. In addition to diseases, Neanderthals and ourselves share a susceptibility towards certain cancers. A study by David Frayer analyzed a rib bone from Krapina, Croatia and found fibrous dysplasia. This type of cancer is still found in the modern population 120 thousand years later. “They probably were sleeping in caves with burning fires...inhaling a lot of smoke...So the air was not completely free of pollutants.” -David Frayer. It is remarkable that we can come to find such similarities with Neanderthals, even if it is only to understand the pain of a disease shared in common.

Over the course of thousands of years, the internal structure of our bodies was slowly reformatted by our genetic interaction with Neanderthals. As our internal bodies changed, so did our epidermal layer. We inherited the BNC2 gene from Neanderthals, this gene specifically deals with skin pigmentation. This discovery implies we Homo Sapiens inherited our pale skin from Neanderthals! This genetic change took thousands of years to fully take hold, beginning its spread throughout European humans at most only 7 kya. In addition to inheriting genes for pale skin, we also inherited the gene for red hair from our Neanderthal cousins. The level of our shared genetic heritage has been fluctuating as well, slowly decreasing as time marches on. Otzi, the Ice-Man, who died around 5.3 kya in the Alps, shares more DNA with Neanderthals than modern Alpine humans. Thousands of years after the extinction of the Neanderthals, the last remnant of their time on earth, their genes, slowly recedes from the world.

A model of Otzi

Pandora's box has been opened, and 3 billion base pairs fell out. The small steps we've made in the last 4 years have shown great advances in both our technological limits and our understanding of Neanderthals. The provisional reconstruction of the Neanderthal and Denisovan epigenome this year (in 2014) is the first step towards an entirely new science. The researchers in that study have already planned to reconstruct the epigenome of Natufians to see how early agriculture effected our epigenome. Whatever they find, it will not be boring. If diseases such as autism and schizophrenia turn out to be a human-unique phenomenon, it would add interesting detail to the evolutionary history of our frontal lobe. All of this changes how we see ourselves – what makes us human is not only the usual suspects (such as brain size or language), but also our mental health and our epigenome. This field of research is incredibly new and fast paced...so watch out! It may all be completely different in 5 years.

Svante Paabo and the skull of a rival geneticist

Their Bones and Body

The Neanderthal genome is a beautiful example of what can be reconstructed from the fossil record, but our search for information does not end there, don't discount the bones! The majority of what we understand about Neanderthals comes from their fossils, and to understand the Neanderthal mind we must ask what is so special about their bones? Neanderthal bones are similar to human weight lifters, not bulky but wiry. Their bones were shorter, denser, thicker, stronger than ours – very well adapted to a life of strenuous activity. Their bones are also more effected by osteoarthritis than ours. Neanderthals lived a brutish life comparatively, 2/3rds are dead by age 30. The maximum age of Neanderthals is 45-50, and by that time their bodies were as run-down as an elderly human. Neanderthals also had larger brains than humans, which strangely enough has no bearing on intelligence. In fact, “more of the Neanderthal brain appears to have been dedicated to vision and body control, leaving less brain to deal with other functions like social networking.” -Eiluned Pearce. On the outside of the body, genetics has shown that Neanderthals would be pale skinned and some had red hair. A 2007 genetic study found that Neanderthals had a version of the MC1R gene, which helps us produce more vitamin D and absorb more calcium from food. While that trait is certainly beneficial, the gene also gives us red hair! In humans this varies between red and dark hair (blond hair is a different genetic change). Sadly we don't know all the genes which contribute to pigmentation, so any assertion is only a likelihood and far from certain.

A computer illustration of the facial geometry of a Neanderthal compared to modern Homo Sapiens

A reconstruction of Shanidar 1, by paleoartist John Gurche

A model of a Neanderthal presumably experiencing happiness. From the Neanderthal Museum in Mettmann, Germany

This pale red headed stocky fellow was also kind of short. 27 limb bones from Atapuerca (near Burgos) Spain were examined in a 2012 study by Carretero Diaz to estimate the height of Pleistocene hominins. Heidelbergensis were a little taller than Neanderthals, with the average Neanderthal height being 5'3”. Heidelbergensis and Neanderthals were a similar height to modern Mediterranean humans. In fact, most hominins stayed about the same size for around 2 million years (Habilis in Africa, Georgicus in Georgia, Floresiensis in Indonesia were short and the exceptions to the rule). While the average height stayed the same, “Amongst every population we have found a tall or very tall individual.” -Researchers with the study. Our Homo genus stayed the same height until about 200 kya when African Sapiens made their entrance to the scene. We were significantly taller on average than all of our predecessors, a hunting band of Homo Sapiens must have been quite a sight to a short Neanderthal. “The explanation is found in the overall morphological change in the body biotype that prevailed in our species compared to our ancestors. The Homo Sapiens had a slimmer body, lighter bones, longer legs, and were taller.” -Researchers with the study.

A height comparison of Heidelbergensis, Neanderthals, and Homo Sapiens, from Plataforma SINC

A model reconstruction of a Neanderthal (named Wilma) from the El Sidron Cave in Spain, next to a living Homo Sapiens (named Marina Allende)

The changes in our body morphology were extremely helpful...we had better thermoregulatory, obstetric, and nutritional systems. Overall we had definite increases in endurance and energy. “Larger legs, narrower hips, being taller and having lighter bones not only meant a reduction in body weight (less muscular fat) but a bigger stride, greater speed, and a lower energy cost when moving the body, walking, or running.” -Carretero Diaz. This extreme physical gap between us and them put Neanderthals at quite the disadvantage, which we will examine later. 

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