ANTH Final: PART1 - Modern Humans and Archaic Hominins

Q: What is ancient DNA?
A: Ancient DNA (aDNA) is genetic material obtained from the remains of organisms that lived in the past, such as bones, teeth, or preserved tissues. It is often thousands of years old and highly degraded.

Q: What is something that creates difficult challenges for working with aDNA (e.g., sample degradation, contamination with modern DNA)?
A: Major challenges include degradation of the DNA over time, making it fragmented and chemically altered, and contamination from modern DNA during excavation or lab work, which can obscure true ancient sequences.

Q: Who were the “Denisovans”?
A: The Denisovans were a group of archaic humans closely related to Neanderthals, identified primarily through DNA analysis of fossils found in Denisova Cave in Siberia.

Q: How do we know that they existed?
A: Their existence is known from ancient DNA extracted from fossil remains (like a finger bone and molar) that revealed a unique genetic lineage distinct from Neanderthals and Homo sapiens.

Q: What was their relationship to Neanderthals and to Homo sapiens?
A: Denisovans and Neanderthals were sister groups that split from a common ancestor after diverging from Homo sapiens. All three groups interbred at various points in history.

Q: What parts of the world did they inhabit, and in what regions do we now find the strongest impact of their genetic legacy in modern people?
A: Denisovans inhabited parts of Asia, including Siberia and possibly Southeast Asia. Their strongest genetic legacy is found in modern populations of Melanesia, Papua New Guinea, Aboriginal Australians, and some Southeast Asians.

Q: When researchers first found evidence of interbreeding between Neanderthals and modern humans and introgression of Neanderthal DNA into modern human genomes, they reported that no evidence existed of introgression (what is this?) of Neanderthal DNA into African people. Is this still the case?
A: No, this is no longer the case. Recent research has found low levels of Neanderthal DNA in African populations, likely due to back-migration from Eurasia after interbreeding occurred there.

Q: If it isn’t, but Neanderthals did not interbreed with people in Africa (no evidence for their presence there exists), how could the DNA have gotten into Africans?
A: The Neanderthal DNA in Africans likely came from non-African humans who had interbred with Neanderthals outside Africa and then migrated back, introducing Neanderthal DNA into African gene pools.

Q: Do we have any evidence for selection against introduced Neanderthal or Denisovan variants?
A: Yes, many Neanderthal and Denisovan genetic variants appear to have been selected against, possibly because they were harmful or incompatible with the Homo sapiens genome, and have been reduced over time.

Q: For positive selection in favor of others?
A: Yes, some archaic variants were beneficial and positively selected. These include genes involved in immunity, skin pigmentation, and environmental adaptations, such as those for high-altitude survival.

Q: Why might disease be important here?
A: Disease likely played a major role in selection: archaic genes that enhanced immunity to new pathogens in non-African environments would have provided a survival advantage to early humans.

Q: Genes involved in physiological processes like dealing with high altitude conditions?
A: Yes, for example, the EPAS1 gene variant found in Tibetan populations, which aids in adaptation to high altitudes, is believed to have been inherited from Denisovans.

Q: What parts of the world did Neanderthals inhabit?
A: Neanderthals lived across Europe and parts of western and central Asia, ranging from Spain to Siberia.

Q: Where did they encounter (or where might they have encountered) Denisovans?
A: Neanderthals and Denisovans likely encountered each other in Central and Eastern Asia, particularly in the Altai region of Siberia where both types of remains have been found.

Q: Same questions for Neanderthal/Homo sapiens encounters.
A: Neanderthals and Homo sapiens likely encountered each other in the Middle East and Europe. These encounters occurred after modern humans migrated out of Africa and led to interbreeding.

Q: Why does phylogenetic analysis of mitochondrial DNA variation in modern humans support the hypothesis that Homo sapiens originated in Africa?
A: Mitochondrial DNA shows the greatest genetic diversity in African populations, suggesting a longer evolutionary history there. All non-African mitochondrial lineages are derived from a subset of African lineages, supporting an African origin.