Q47 - Neanderthal Ancient DNA and Gene Flow

Theoretical 2 Real exam question - full text reproduced under IBO's CC BY-NC-SA 4.0 license

Human Evolution & Hominid Phylogeny Molecular Evolution & Neutral Theory

The 2022 Nobel Prize was awarded for sequencing ancient DNA to study the human past. This work produced whole genomes of several Neanderthals and one Denisovan (another group of archaic hominins).

The figure depicts trees showing phylogenetic relationships between those archaic specimens and different groups of modern humans.

Figure 1. Cladograms based on mitochondrial DNA sequence (a), and average genetic distances across autosomal genomes (b).

Modern humans are represented by 2 African (A1, A2) and 2 Eurasian (E1, E2) individuals. Archaic hominins are represented by 3 Neanderthals (N1, N2, N3) and one Denisovan (D1). Numbers in brackets next to archaic hominins indicate the approximate age (in thousands of years ago) of each specimen.

Note: Branch length is arbitrary and conveys no information here.

The split between modern humans and Neanderthals occurred 750-550 thousand years ago. 60-50 thousand years ago, there was a Neanderthal-to-human gene flow event, which occurred in Eurasia (so did not affect African human populations). All non-African modern humans have 2-3% Neanderthal DNA derived from that gene flow event.

However, present-day humans also have sequence segments similar to Neanderthals’ because of common human-Neanderthal ancestry, and not just because of gene flow. This phenomenon is called “Incomplete Lineage Sorting” (ILS).

Cladograms based on mitochondrial DNA (a) and autosomal genome distances (b) for modern humans, Neanderthals, and Denisovan

True or False?

Q47.1. Neanderthal-like sequences in present-day humans, which result from gene flow, are on average shorter (fewer base pairs long) than those resulting from ILS.

Q47.2. If branch length in tree b was proportional to the number of accumulated mutations, the branch leading to N2 would be expected to be shorter than the branch leading to N1.

Q47.3. A possible explanation for the difference between the mitochondrial and autosomal trees is a gene flow event from humans to Neanderthals between 400 and 120 thousand years ago, that resulted in human-like mitochondrial DNA being introduced into the gene pool of Neanderthals.

Q47.4. By combining Neanderthal-like sequence segments from many (>100) unrelated modern humans, one can only recover around 2-3% of the whole Neanderthal genome.

Q47.5. The maximum frequency of any Neanderthal allele in any present-day non-African population is 3%.

Q47.6. Neanderthal-like segments in present-day humans are expected to have identical sequences to the corresponding genome segments of the N1 specimen.

Q47.7. Present day Africans share no alleles in common with Neanderthals.

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Question reproduced from IBO 2023, Theoretical Paper 2, licensed under CC BY-NC-SA 4.0 - attributed to the International Biology Olympiad. Open the full exam PDF