The human genome shares approximately ~96% identity with the chimp genome. One scientist proposes that humans are unique because a receptor kinase TPK1 is evolving rapidly in humans. Describe the experiments that could lead the scientist to this conclusion.

What is the scientist’s hypothesis about the TPK1 gene

[That the receptor kinase TPK1 is evolving rapidly in humans.]

What is the first step in testing this hypothesis

[Compare the TPK1 protein sequences from humans and chimpanzees.]

How is the protein sequence comparison conducted

[By obtaining TPK1 gene sequences from both species, translating them into amino acid sequences, and identifying differences.]

Why is comparing human and chimpanzee genes useful

[Because they share about 99% identity in their genes, making even subtle differences significant.]

What types of genetic substitutions are identified in the analysis

[Synonymous and non-synonymous substitutions.]

What is a synonymous substitution

[A DNA change that does not alter the amino acid sequence of the protein due to genetic code redundancy.]

What is a non-synonymous substitution

[A DNA change that alters the amino acid sequence of the protein.]

Why are non-synonymous substitutions important

[They may be under selection and indicate functional changes in the protein.]

What ratio is used to assess selective pressures on TPK1

[The Ka/Ks ratio (also known as dN/dS).]

What does Ka (or dN) represent

[The rate of non-synonymous substitutions per non-synonymous site.]

What does Ks (or dS) represent

[The rate of synonymous substitutions per synonymous site.]

How is the Ka/Ks ratio calculated

[By dividing Ka by Ks.]

What does a Ka/Ks ratio > 1 indicate

[Positive selection, where amino acid changes are favoured and indicate rapid evolution.]

What does a Ka/Ks ratio < 1 indicate

[Purifying selection, where amino acid changes are generally harmful and selected against.]

What does a Ka/Ks ratio ≈ 1 suggest

[Neutral evolution, where changes are neither beneficial nor harmful.]

How can the scientist test if TPK1 evolution is specific to humans

[By comparing the Ka/Ks ratio for TPK1 between humans and a more distant species like macaque.]

Why compare with macaques

[They are a more distant primate relative, and differences in substitution rates between species can reveal lineage-specific evolution.]

How does comparing human-macaque vs chimp-macaque help

[It helps identify whether accelerated evolution occurred specifically in the human lineage.]

What other genomes should be included to confirm human-specific changes

[Neanderthal and Denisovan genomes.]

Why include Neanderthal and Denisovan sequences

[To determine whether the positively selected amino acid changes in modern humans are absent or rare in these extinct relatives.]

What would support the idea of human-specific TPK1 evolution

[If derived amino acid changes are fixed or common in modern humans but absent in Neanderthals and Denisovans.]

What does identifying “derived” vs “ancestral” alleles help with

[It helps determine whether specific changes are unique to modern humans.]

How would a Ka/Ks > 1 specifically in humans support the hypothesis

[It would indicate rapid, positive selection acting uniquely on the TPK1 gene in the human lineage.