Deep in Human DNA, a Gift from the Neanderthals

Unbeknownst to most, the innate defense built in the human body may have come from the early ancestors of the Neanderthals. People of Asian or European descent have some Neanderthals DNA due the the amount of breeding between the modern humans and the Neanderthals long ago. The reason those genes have stuck around through time is due to the possibility of being the reason humans are protected against infections.

As modern humans expanded from Europe and Asia, they "encountered new viruses", possibly from the Neanderthals but also were protected from these same viruses due the the defenses the Neanderthals gave them.

The immune system of a human is quite complex, and in order to learn more about such a "glimpse at the distant medical history of our species", an evolutionary biologist, David Enard, first had to change his approach to the task: starting with finding all the proteins human have that "interact with at least one virus." This reason for this approach being that viruses cannot duplicate singularly: they need a host protein to inject their DNA into and it replicate with the virus DNA.

Dr. Enard discovered that the proteins humans have, "many have changed over the course of evolution" and because of this, he began to wonder how then Neanderthal genes are still somewhat around in the modern human genome. Those particular genes must provide some evolutionary advantage, for which they have been selected for over time. Researchers believe that the beneficial Neanderthal genes were "borrowed" by the modern human to fight infections, and more specifically code for "proteins that interact with viruses." By analyzing the genomes of living humans today, it is clear that many proteins made by these genes mostly interact with only influenza, others only H.I.V. Although those diseases did not directly come from the Neanderthals today, the defense their genes gave humans years ago is still somewhat relevant in humans today.
I am not sure to the extent of which I believe the content in this article. Sure, the innate defense system of the immune system had to come from somewhere, but this seems a little far-fetched. It does makes sense though that if in fact the immune system was due to the modern human interbreeding with Neanderthals, those genes inherited for defense have evolved over time and changed, with the amount of their DNA declining over time.
https://www.nytimes.com/2018/10/04/science/neanderthal-genes-viruses.html
http://humanorigins.si.edu/evidence/human-fossils/species/homo-neanderthalensis
https://www.huffingtonpost.com/quora/what-do-evolutionary-biol_b_3644482.html

A single gene mutation that allowed humans to become optimal long-distance runners

There are various evolutionary changes that allowed early hominids to transition from "forest dwellers to life primarily upon the arid Savannas of Africa"(1). Some of these changes were the pelvis becoming bowl-shaped, the first digit on the foot becoming opposable and having a larger calcaneus. These few skeletal changes greatly increased the comfort of upright walking eventually leading to a lifestyle suitable for becoming hunter-gathers. However, it has been recently proposed that a mutation that leads to the lack of the CMAH gene was a needed change to allow early hominids to improve long distance running. More specifically, the researchers who came to this conclusion saw that when mice lacked the same gene that they "displayed greater resistance to fatigue, increased mitochondrial respiration and hind-limb muscle, with more capillaries to increase blood and oxygen supply"(1). Also, it is interesting to note that due to the mutation of CMAH, N-glycolylneuraminic acid, a sialic acid, was loss as well. The importance of this is that certain sialic acids can increase type 2 diabetes and possibly cancer from the consumption of red meat. Ultimately, the mutation of the CMAH gene gave a selective advantage to early hominids to allow them to employ the use of persistent hunting.

Having a slight background in biodiversity and evolution, I found it interesting to read more about the changes necessary to further diverge from chimpanzees. I knew of the physical changes that allowed early hominids to go from knuckle walkers to walking on two feet, but I had not thought much about the genetic changes. To further educate myself, I looked up what exactly persistent hunting is and how it works. The reason it was so effective was because humans had the ability to walk, run and track prey with great endurance. However, what was new to me was the fact that most prey had to pant, slow down or stop completely to recuperate while humans can recuperate while sweating on the go. Furthermore, the hunt can last hours, possibly all through the afternoon, as early hominids chased their prey through the scorching heat in the Savannas. If you have the time, I suggest watching this video as it gives a great glimpse of what our early ancestors had to do to secure food. Surprisingly, there are still people today who hunt in this fashion as the video will show you. Keep in mind that this man has shoes, a water bottle and a spear with a steel tip and it took him 8 hours. I can only imagine how long it would take someone having to run barefoot through brush and cacti while learning a new technique of acquiring food. Lastly, I am curious what even led early hominids to adapt this mode of obtaining food. Who decided that running for long distances would eventually pay off (high cognitive risk-reward computation), better yet, that chasing meat was smart? Mind you, the idea of walking or running was relatively new and meat/insects only account for at most 9-12% of a chimpanzees diet.

Why Don't Humans Have Much Neanderthal DNA in Them?

A long time ago, Neanderthal's and modern day humans diverged from a common ancestor, but only 1 of the 2 species did well.  The neanderthals did not just get wiped off the earth, since about 50,000 years ago, they interbred with modern humans as they were leaving Africa, leaving a small amount of their DNA behind.  And by small, I mean very small.  The question is, why is there such a small amount of DNA left over by the neanderthals, and why did the neanderthal human hybrids not survive well?  One answer is as simple as population size.  In smaller populations, natural selection is not as strong of a factor in the population, and so the neanderthals were subject to a lot of inbreeding, and overall the entire population developed and spread more and more mutations around within themselves.  Since these mutations did not stop them from breeding with each other, it can be assumed that all of these mutations built up, and eventually became a very large problem for  neanderthals.

This information also shows why not much neanderthal DNA remains in modern day humans.  Since the neanderthals already were so heavily mutated, when they bred with humans, they passed along their mutations to the hybrid offspring, who then either would have died from the mutations, or would have then passed them down again to their offspring, and so on.  Overtime this process makes it so that the small amount of DNA that was transferred from neanderthal to human was slowly lost, but not completely, resulting in a very small amount of their DNA found in modern humans.

I'm a little surprised that the answer to this problem is so simple.  All it really has to do with is population size, and I think that that is really interesting.  Granted the small population size does make a lot of sense, I didn't think to take into account that this means that there would be a lot of inbreeding occurring among the population, which also makes a lot of sense.  It is also pretty interesting that because of this initial inbreeding, that the major effects of it made the neanderthal human hybrids less likely to survive, and so the amount of neanderthal DNA in modern humans is so small.

http://www.nytimes.com/2016/11/09/science/neanderthal-dna-natural-selection.html?rref=collection%2Fsectioncollection%2Fscience&action=click&contentCollection=science&region=stream&module=stream_unit&version=latest&contentPlacement=58&pgtype=sectionfront 

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006340

First Analysis of Y Chromosome in Neanderthals

          This article was very interesting from Fernando L. Mendez. This was the first study to observe the Y chromosome in Neanderthals. I think it is very interesting that previous studies only sequenced DNA from fossils of Neanderthal woman or mitochondrial DNA (which is only passed down to either sex from the mother). The Y chromosome can carry so many different genes and traits that the female sex chromosome cannot. In this case, they found protein-coding differences between genes in humans and Neanderthals on the Y chromosome which were mutations known in humans to create male-specific minor histocompatibility antigens. The Y chromosome was the main part of the Neanderthal genome that needed to be analyzed. This comes as a shock to me to be honest. Studying the Y chromosome helps scientists understand the population divergence between Neanderthals and modern humans, as well as observe possible genetic interactions between archaic and modern gene variations between hybrid offspring.  The thing that surprises me the most is how much time it took for this to happen. This started almost as far back as 2008. I would think that both sex chromosomes would be analyzed. I am curious to know why there was such a long wait for the Y chromosome. Was there not such a demand to analyze it right away? Did the technology at hand not have the skills to work on it? 

Humans mated with Neandertals much earlier and more frequently than thought

Members of our species had sex with Neanderthals much earlier and more often than previously believed, according to a new study of ancient DNA. As some of the first bands of modern humans moved out of Africa, they met and mated with Neanderthals about 100,000 years ago perhaps in the Nile Valley, along the coastal hills of the Middle East, or in the Arabian Peninsula. This pushes back the earliest encounter between the two groups by tens of thousands of years and suggests that our ancestors were shaped in significant ways by swapping genes with other types of humans.

These early modern humans have since died out and are not among the ancestors of people living today but a small bit of DNA survived in a toe bone of a neanderthal woman who lived 50,00 years ago in Denisovan cave in the Altai mountains of Siberia, Russia. An analysis of her ancient genome has found inherited DNA from modern humans in Africa, including a gene that may involved speech.

This is the first genetic evidence found that shows modern humans mated with neanderthals, but what did this mating mean for us today?

The levels of DNA found suggested these mating encounters happened in one generation over a short period of time, but it was enough to pass on genes that may have been the difference between survival and extinction for modern humans. The genes that were possibly passed down could of been involved in speech, immune system, and the production of sperm - fitting the theory that interbreeding was an important source of genetic diversity that is crucial for adapting to new terrain as modern humans spread into foreign lands.

Maybe without these interactions between modern humans and neanderthals us as a human race would be a lot different.