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Sunday, March 5, 2023

Our Ancestors So Long Ago: Neanderthal, Denisovian: All Found in a Kebara Cave in Israel

 Nadene Goldfoot                                                


                         Neanderthal Remains in Kebara, Israel 

Kebara, paleoanthropological site on Mount Carmel in northern Israel that has yielded a trove of Neanderthal bones and associated artifacts.

The Kebara cave was occupied by humans and various other animals from the Middle Paleolithic Period (approximately 200,000 to 40,000 years ago) through the Upper Paleolithic Period (about 40,000 to 10,000 years ago). The more-recent Upper Paleolithic and Holocene levels of the site, known as the Kebaran and Natufian levels, were excavated in the 1930s. They contained a series of human burials plus a number of partially cremated remains. The Middle Paleolithic levels were excavated in the 1960s and 1980s. They are exceptionally rich in archaeological remains, including multiple layers of large flat hearths, Middle Paleolithic tools, and animal bones, in addition to two infant skeletons, a young adult skeleton (known as Kebara 2) that dates to about 60,000 years ago, and fragments of many more individuals. The infant and adult skeletons were clearly interred intentionally, although burial pits could not be discerned. Of the fragile fragmentary infant fossils, only their teeth indicate that they were Neanderthals.              

We have 5 basic  senses for reasons of staying alive.  They help to alert us of our surroundings and danger.  Sight, smell, taste, touch, hearing.  Animals are born with these same senses as well, with far better abilities than ours to make up for our ability to reason far better than they. A dog's sense of hearing and smell are so much better than ours; no wonder they are man's best friend.   These senses helped our primitive ancestors to stay alive and improve within each century of life.  Neuroscientists are well aware that we are a bundle of senses. Many would argue that we have anywhere between 22 and 33 different senses. Some animals of today have senses we don't have such as polarized light.  Polarized light is one – many animals, including insects and birds, use polarized light to decide which direction to go in. 

Neanderthal, (Homo neanderthalensis, Homo sapiens neanderthalensis), also spelled Neandertal, member of a group of archaic humans who emerged at least 200,000 years ago during the Pleistocene Epoch (about 2.6 million to 11,700 years ago) and were replaced or assimilated by early modern human populations (Homo sapiens) between 35,000 and perhaps 24,000 years ago.  

Compared with modern humans, Neanderthals had a more robust build and proportionally shorter limbs. Researchers often explain these features as adaptations to conserve heat in a cold climate, but they may also have been adaptations for sprinting in the warmer, forested landscape that Neanderthals often inhabited. Nonetheless, they had cold-specific adaptations, such as specialised body-fat storage enlarged nose to warm air (although the nose could have been caused by genetic drift). Average Neanderthal men stood around 165 cm (5 ft 5 in) and women 153 cm (5 ft 0 in) tall, similar to pre-industrial modern humans. The braincases of Neanderthal men and women averaged about 1,600 cm3 (98 cu in) and 1,300 cm3 (79 cu in) respectively, which is considerably larger than the modern human average. The Neanderthal skull was more elongated and had smaller parietal lobes and cerebellum, while the Neanderthal brain was larger in the temporal, occipital, and cerebellar regions, indicating differences in brain development between the two species.

Approximately 20 percent of Neanderthal DNA survives in modern humans; however, a single human has an average of around 2% Neanderthal DNA overall with some countries and backgrounds having a maximum of 3% per human. (I have 2% according to DNA testing with 23&Me.) 

                                               
                                


Modern human genes involved in making keratin, a protein constituent of skin, hair, and nails, contain high levels of introgression. For example, the genes of approximately 66% of East Asians contain a POUF23L variant introgressed from Neanderthals, while 70% of Europeans possess an introgressed allele of BNC2. Neanderthal variants affect the risk of developing several diseases, including lupusbiliary cirrhosisCrohn's disease, type 2 diabetes, and SARS-CoV-2. The allele of MC1R linked to red hair in Neanderthals is not found in Europeans, but is present in Taiwanese Aborigines at a frequency of 70% and at moderately high frequencies in other East Asian populations; hence, there is no evidence Neanderthals had red hair.  (King David was mentioned in Torah to be a gingy-having red hair-so no Neanderthal in him? ).  While interbreeding is viewed as the most parsimonious interpretation of these genetic findings, the 2010 research of five present-day humans from different parts of the world does not rule out an alternative scenario, in which the source population of several non-African modern humans was more closely related than other Africans to Neanderthals because of ancient genetic divisions within early Hominoids.

Le Moustier Neanderthal skull reconstruction, Neues Museum Berlin[23]

Research since 2010 refined the picture of interbreeding between Neanderthals, Denisovans, and anatomically modern humans. Interbreeding appears asymmetrically among the ancestors of modern-day humans, and this may explain differing frequencies of Neanderthal-specific DNA in the genomes of modern humans.


Denisovans are a new find of humanoids..  Denisovans apparently interbred with modern humans, with the highest percentages (roughly 5%) occurring in MelanesiansAboriginal Australians, and Filipino Negritos. This distribution suggests that there were Denisovan populations across Eurasia, the Philippines, and New Guinea and/or Australia, but this is unconfirmable. Introgression into modern humans may have occurred as recently as 30,000 years ago in New Guinea, which, if correct, might indicate this population persisted as late as 14,500 years ago. There is also evidence of interbreeding with the Altai Neanderthal population, with about 17% of the Denisovan genome from Denisova Cave deriving from them. A first-generation hybrid nicknamed "Denny" was discovered with a Denisovan father and a Neanderthal mother. Additionally, 4% of the Denisovan genome comes from an unknown archaic human species which diverged from modern humans over one million years ago.

In 2014, researchers introduced a novel method based on epigenetics—a set of molecular knobs that can turn gene expression up or down—to analyze gene regulation in long-extinct hominins. One such knob is a chemical modification called methylation, which silences gene expression. In methylated DNA, one nucleotide, cytosine, degrades over thousands of years into a different end product than usual. By tracking that degradation in an ancient genome, scientists can create a methylation "map.

                Liran Carmel(Hebrew: לירן כרמל, born August 7, 1971) is an Israeli scientist, professor of computational biology at the Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem. Carmel is the Snyder Granadar Chair for Genetics, and is the 2021 Massry Prize laureate for his studies in the field of ancient DNA.  Carmel was born and raised in Israel. He studied for a B.Sc. in physics in the Academic Atuda, and served in the military as a physicist in Rafael Advanced Defense Systems Ltd. During his military service, he obtained his M.Sc. degree in quantum mechanics at the Technion - Israel institute of technology, under the supervision of Ady Mann. After his military service, Carmel completed his Ph.D. degree in mathematics and computer science at the Weizmann Institute of Science, under the supervision of David Harel. In his Ph.D. Carmel developed algorithms for odor coding and digitization, and was head of the algorithms team in a company that developed means for computerized odor transmission. In 2004, Carmel went to the United States for postdoctoral studies at the National Institutes of Health (NIH) in Bethesda, Maryland, where he specialized in molecular evolution in the research group of Eugene Koonin.
Dr. David Gokhman:  
When it comes to genetic adaptations, humans are unique. Though these adaptations came with advantages like the ability to walk upright and complex brains, they also brought with them many human-specific diseases—Alzheimer’s, schizophrenia, and more. To understand why these adaptations came at such a high price, Dr. David Gokhman, who recently joined the Department of Molecular Genetics, is searching for the adaptations that set humans apart, by comparing human genes to those of two close relatives—the extinct Neanderthal and Denisovan species, and the great apes. Dr. David Gokhman completed his BSc, magna cum laude, in 2011 at the Hebrew University of Jerusalem, with a major in biology and a minor in chemistry. He also earned his MSc (2012) and PhD (2018) degrees in the Department of Genetics at the Hebrew University. He conducted postdoctoral research at Stanford University, and joined the faculty of the Weizmann Institute in 2021. Dr. Gokhman’s awards and recognitions include the Mochrik Prize for outstanding students in 2014, the Dan David Young Researcher Award in 2017, and the Hans Wiener Prize for best doctoral thesis, in 2018. His research earned the title of “Breakthrough of the Year” both in Archaeology magazine in 2014, and in Science magazine in 2019 (people’s choice). He also made The Marker magazine’s “40 Under 40” list in 2020. Before attending Hebrew University, Dr. Gokhman worked as the head of the data mining team at the Prime Minister’s Office, and was the recipient of the Israel Defense Prize for exceptional technological breakthroughs in 2008.

"Liran Carmel and David Gokhman, geneticists at the Hebrew University of Jerusalem, and their colleagues applied this method to DNA in the girl's pinkie from Denisova Cave. They compared the girl's methylation map with similar maps of modern humans, Neanderthals, and chimpanzees, focusing on areas where the degree of methylation differed by more than 50%.The method can't provide exact body measurements. "We can say [Denisovans had] longer fingers [than modern humans for example], but we cannot say 2 millimeters longer," Carmel explains. In total, the researchers discovered 56 Denisovan anatomical features that may have differed from humans or Neanderthals, 34 of them in the skull. As expected, the Denisovan girl looked fairly similar to a Neanderthal, with a similarly flat cranium, protruding lower jaw, and sloping forehead, the researchers report this week in Cell.Yet she also had key differences. The reconstructed face was notably wider than that of a modern human or Neanderthal, and the arch of teeth along the jawbone was longer.

WASHINGTON - Next time you call someone a Neanderthal, better look in a mirror. Many of the genes that help determine most people's skin and hair are more Neanderthal than not, according to two new studies that look at the DNA fossils hidden in the modern human genome.  About 50,000 years ago, modern-day humans migrated out of Africa north to Europe and East Asia and met up with furrow-browed Neanderthals that had been in the colder climates for more than 100,000 years. Some of the two species mated. And then the Neanderthals died off as a species - except for what's left inside of us.  In some places, such as the DNA related to the skin, the genetic instructions are as much as 70 percent Neanderthal and in other places there's virtually nothing from the species that's often portrayed as brutish cavemen. 

The difference between where Neanderthal DNA is plentiful and where it's absent may help scientists understand what in our genome "makes humans human," said University of Washington genome scientist Joshua Akey, lead author of the paper in Science. After sequencing the Neanderthal genome, scientists discovered all present day non-African individuals carry some Neanderthal ancestry in their DNA. Now, researchers at Princeton University present evidence of Neanderthal ancestry in African populations too, and its origin provides new insights into human history.  When the first Neanderthal genome was sequenced, using DNA collected from ancient bones, it was accompanied by the discovery that modern humans in Asia, Europe and America inherited approximately 2% of their DNA from Neanderthals — proving humans and Neanderthals had interbred after humans left Africa. Since that study, new methods have continued to catalogue Neanderthal ancestry in non-African populations, seeking to better understand human history and the effects of Neanderthal DNA on human health and disease. A comparable catalogue of Neanderthal ancestry in African populations, however, has remained an acknowledged blind spot for the field due to technical constraints and the assumption that Neanderthals and ancestral African populations were geographically isolated from each other.

In a paper published today in the journal Cell, a team of Princeton researchers detailed a new computational method for detecting Neanderthal ancestry in the human genome. Their method, called IBDmix, enabled them for the first time to search for Neanderthal ancestry in African populations as well as non-African ones. The project was led by Joshua Akey, a professor in Princeton’s Lewis-Sigler Institute for Integrative Genomics (LSI). The studies mostly examined the genomes of people whose ancestors left Africa at some point.

People whose ancestors have all stayed in Africa have almost no Neanderthal DNA because there was little interbreeding.

    Benjamin Vernot: University of Washington Seattle | UW · Department of Genome Sciences

 Vernot and Akey (2015) concluded the greater quantity of Neanderthal-specific DNA in the genomes of individuals of East Asian descent (compared with those of European descent) cannot be explained by differences in selection. They suggest "two additional demographic models, involving either a second pulse of Neanderthal gene flow into the ancestors of East Asians or a dilution of Neanderthal lineages in Europeans by admixture with an unknown ancestral population" are parsimonious with their data.

Admixture occurs when individuals from two or more previously isolated populations interbreed  The previously isolated populations are referred to as ancestral or parental and the newly formed population is referred to as admixed. In non-human species, the same process is often referred to as hybridization.

We Jews are an endogamous society, having interbred withindiffering generations because of countries isolating them fromtheir population such as the ghetto system.    Ashkenazi Jews have historically been an endogamous population. Marrying within the group remains important to many Jews because endogamy is seen as one way to preserve Judaism and ensure the survival of future generations.  


Resource:

https://www.cbsnews.com/news/modern-humans-more-neanderthal-than-once-thought-studies-suggest/

https://www.britannica.com/place/Kebara

https://www.weizmann.ac.il/WeizmannCompass/sections/new-scientists/dr-david-gokhman

https://en.wikipedia.org/wiki/Liran_Carmel

https://www.britannica.com/place/Kebara

https://www.science.org/content/article/ancient-dna-puts-face-mysterious-denisovans-extinct-cousins-neanderthals

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556814/#:~:text=Admixture%20occurs%20when%20individuals%20from,often%20referred%20to%20as%20hybridization.https://www.progress.org.uk/marry-out-some-surprising-consequences-of-genetic-disease-risk-among-ashkenazi-jews/#:~:text=Ashkenazi%20Jews%20have%20historically%20been,the%20survival%20of%20future%20generations.

https://en.wikipedia.org/wiki/Neanderthal_genetics

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