Podcast
Questions and Answers
Which population has the highest percentage of Neanderthal DNA according to the data?
Which population has the highest percentage of Neanderthal DNA according to the data?
What chromosome was found to contain very little Neanderthal DNA?
What chromosome was found to contain very little Neanderthal DNA?
What is the primary reason for the variation in Neanderthal DNA percentage among different populations?
What is the primary reason for the variation in Neanderthal DNA percentage among different populations?
Which of the following groups has been shown to completely lack Neanderthal DNA?
Which of the following groups has been shown to completely lack Neanderthal DNA?
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What do the red lines in the analysis represent?
What do the red lines in the analysis represent?
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What percentage of Neanderthal DNA is identical to modern human DNA?
What percentage of Neanderthal DNA is identical to modern human DNA?
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What was the primary source of sequence data in the DNA extracts from Vindija cave?
What was the primary source of sequence data in the DNA extracts from Vindija cave?
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Which of the following was used to conduct additional sequencing of Neanderthal DNA?
Which of the following was used to conduct additional sequencing of Neanderthal DNA?
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Which component was NOT mentioned in relation to Neanderthal genetics?
Which component was NOT mentioned in relation to Neanderthal genetics?
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If two Neanderthal samples have identical mtDNA, what does this suggest?
If two Neanderthal samples have identical mtDNA, what does this suggest?
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How was the Neanderthal genome initially sequenced?
How was the Neanderthal genome initially sequenced?
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How many base pairs of Neanderthal DNA were sequenced in the mentioned study?
How many base pairs of Neanderthal DNA were sequenced in the mentioned study?
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What type of tube is referenced in the context of working with bacteria?
What type of tube is referenced in the context of working with bacteria?
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Why did early research into ancient DNA primarily focus on sequencing mitochondrial DNA (mtDNA)?
Why did early research into ancient DNA primarily focus on sequencing mitochondrial DNA (mtDNA)?
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What is one of the main challenges when attempting to sequence ancient DNA?
What is one of the main challenges when attempting to sequence ancient DNA?
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How did researchers attempt to sequence Neanderthal DNA when sequences were unknown?
How did researchers attempt to sequence Neanderthal DNA when sequences were unknown?
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What is the approximate length of a Neanderthal mitochondrial genome based on published research?
What is the approximate length of a Neanderthal mitochondrial genome based on published research?
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What organism's DNA was extracted from a 38,000-year-old specimen in Croatia for sequencing?
What organism's DNA was extracted from a 38,000-year-old specimen in Croatia for sequencing?
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What does the ring structure in the diagram discussed in the context of DNA represent?
What does the ring structure in the diagram discussed in the context of DNA represent?
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What is the length of human mitochondrial DNA for comparison?
What is the length of human mitochondrial DNA for comparison?
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What was a significant year when a complete Neanderthal mitochondrial genome sequence was published?
What was a significant year when a complete Neanderthal mitochondrial genome sequence was published?
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What percentage of modern human DNA is identical to Neanderthal DNA?
What percentage of modern human DNA is identical to Neanderthal DNA?
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Which population has been found to have Neanderthal introgression in their genomes?
Which population has been found to have Neanderthal introgression in their genomes?
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What is the average size of haploblocks indicating variation in Neanderthals and non-Africans?
What is the average size of haploblocks indicating variation in Neanderthals and non-Africans?
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How much of some modern human genomes have been found to be of Neanderthal origin?
How much of some modern human genomes have been found to be of Neanderthal origin?
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Based on nuclear DNA comparisons, Denisovans are more closely related to which group?
Based on nuclear DNA comparisons, Denisovans are more closely related to which group?
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Where was the first Neanderthal fossil discovered?
Where was the first Neanderthal fossil discovered?
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How long ago did Neanderthals likely disappear?
How long ago did Neanderthals likely disappear?
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What characteristic is NOT associated with Neanderthal skeletal structure?
What characteristic is NOT associated with Neanderthal skeletal structure?
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What is a consequence of genetic bottlenecks?
What is a consequence of genetic bottlenecks?
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What is thought to have contributed to Neanderthal extinction?
What is thought to have contributed to Neanderthal extinction?
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What does bottlenecking refer to in population genetics?
What does bottlenecking refer to in population genetics?
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Which statement is true about Neanderthals and modern humans?
Which statement is true about Neanderthals and modern humans?
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Which factor is debated as a contributor to Neanderthal extinction?
Which factor is debated as a contributor to Neanderthal extinction?
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What percentage of Denisovan DNA is found in Australians?
What percentage of Denisovan DNA is found in Australians?
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Which species is estimated to have lived between ~400,000 to ~30,000 years ago?
Which species is estimated to have lived between ~400,000 to ~30,000 years ago?
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Which feature is notably associated with Homo floresiensis?
Which feature is notably associated with Homo floresiensis?
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What is believed to have occurred between Denisovans and modern humans?
What is believed to have occurred between Denisovans and modern humans?
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Why is less known about the genome of Homo floresiensis?
Why is less known about the genome of Homo floresiensis?
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What is the maximum estimated length of time from which DNA can be recovered?
What is the maximum estimated length of time from which DNA can be recovered?
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What percentage of Denisovan DNA is found in East Africans?
What percentage of Denisovan DNA is found in East Africans?
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Which of these hominin species is not believed to have co-inhabited with Homo sapiens?
Which of these hominin species is not believed to have co-inhabited with Homo sapiens?
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Study Notes
Ancient DNA
- Several archaic hominin species coexisted with Homo sapiens.
- Modern genomic methods allow the study of extinct species' genomes.
- Homo sapiens that left Africa interbred with Neanderthals and Denisovans.
Objectives
- Students will apply concepts like sequencing, population genetics, and organellar DNA to understand archaic genome research.
Schedule
- Monday: Review Session (12:30 PM - 2:00 PM), Lennon 206
- Tuesday: Review Session (2:00 PM - 3:30 PM), Lennon 206
- Wednesday: Final Exam (8:00 AM - 10:00 AM)
Svante Pääbo
- A Swedish geneticist, Svante Pääbo, won the 2022 Nobel Prize in Physiology or Medicine for his work on extinct hominin genomes.
- He was the first to successfully extract and sequence ancient DNA from a Neanderthal.
- Pääbo and his team completed a draft reference sequence of the Neanderthal genome in 2009.
Ancient DNA Study Intersections
- Reference sequences
- Cloning
- Population genetics
- mtDNA
Hominin Species
- Neanderthals: ~400,000 to ~30,000 years ago
- Denisovans: ~400,000 to ~30,000 years ago
- Homo floresiensis: ~100,000 to ~50,000 years ago
Challenges of Ancient DNA
- Very little DNA can be recovered from samples.
- Samples are not easy to come by.
- Ancient DNA is often contaminated from soil microbes and human handling.
- Ancient DNA fragments are degraded. Generally only 100-200 base pairs long.
- Recovery is done in a cleanroom
Early Focus on mtDNA
- Much of the earliest ancient DNA research focused on mitochondrial DNA (mtDNA) sequencing.
- mtDNA's circular structure and higher copy number made it easier to extract from degraded samples.
Sequencing Neanderthal DNA
- A complete Neanderthal mitochondrial genome sequence was published in 2008 (16,565 base pairs).
- DNA was extracted from a 38,000-year-old Neanderthal specimen.
- Neanderthal genomic sequencing involved extracting, cloning, small-scale sequencing, and batch culture steps
Sequencing the Neanderthal Genome
- 95-99% of sequence from DNA extract of Neanderthal samples were determined to be from non-primate origin (mostly microbes).
- A draft of the complete Neanderthal genome was published in 2010; mtDNA from three different samples was compared.
- Neanderthal DNA was found to be 99.7% identical to modern human DNA.
Neanderthals
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First fossil discovered in Neander Valley, Germany (1856)
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Fossils date back ~400,000 years ago; disappeared ~30,000-40,000 years ago.
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Physical features – low, flat, elongated skull, barrel-shaped rib cages, short, bowed shoulder blades.
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Adapted to cold environment; used tools; suffered frequent injuries.
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Range included Europe and southwest and central Asia.
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Co-existed with Modern humans approximately 30,000-40,000 years ago, unclear how much interaction there was.
Bottlenecking
- Neanderthal populations experienced an extended period of bottlenecking (population drastically reduced in size).
- This results in a very low level of genetic diversity and a different frequency of alleles in surviving populations from the original population.
Interbreeding
- If interbreeding occurred, traces of Neanderthal DNA should be present in the descendants.
- Introgression: a transfer of DNA from one species to another through mating.
- Admixture: DNA indicates that different populations interbred.
Determining Neanderthal/Homo Sapien Interbreeding
- Neanderthal sequences were aligned to Homo sapiens genome sequences.
- Neanderthal DNA found in the autosomes of non-African populations; very little found on the X chromosome.
- Worldwide distribution of Neanderthal DNA shows varying percentages (e.g., Europeans 2%, East Asians 3%).
Denisovans
- Discovered in Denisova Cave, Altai Mountains, Southern Siberia.
- Identified in 2010 as representing a new hominin species through mtDNA sequencing.
- Based on nuclear DNA comparisons Denisovans are more closely related to Neanderthals than to modern humans.
- Denisovans shared a common ancestor with Neanderthals about 400,000 years ago.
- DNA from a single Denisovans location shows comparable genetic diversity as that of Neanderthals from Eurasia.
- Interbreeding with modern humans occurred, evidence in DNA of Eurasians and Australians (e.g., Melanesians 5%).
Homo floresienesis
- Estimated to be ~3.5 ft tall.
- Fossils discovered on the island of Flores, Indonesia (2003)
- Small size may be adaptation to limited resources on an island.
- Used stone tools, but little DNA is known.
DNA Degradation
- DNA degrades over time. The maximum length of time DNA can be recovered is about 1 million years.
- Extinct dinosaurs (65 million years ago) have no recoverable DNA.
Reminders for this week
- One more office hour today.
- No more late assignments will be accepted.
- Review sessions on Monday and Tuesday in Lennon 206.
- Final exam on Wednesday, December 11th at 8:00am.
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Description
Test your knowledge on Neanderthal DNA, its variation among populations, and the significance of genetic findings. This quiz covers questions related to Neanderthal percentages, chromosome analysis, and sequencing methods, providing insights into ancient human relatives and their genetic legacy.
