Hudson-Kreitman-Aguade test

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What does the McDonald-Kreitman (MK) test compare to determine if a gene is evolving neutrally?

The ratio of non-synonymous to synonymous substitutions within a species and the ratio between species

The number of polymorphic differences within a species and the number of fixed differences between species

The rate of non-synonymous and synonymous substitutions within a species

The rate of evolution within a species and the rate of evolution between species (correct)

According to the neutral theory of molecular evolution, what should be true about the evolutionary rate of a gene?

The evolutionary rate should be constant both within and between species (correct)

The evolutionary rate should be variable within a species but constant between species

The evolutionary rate should be variable both within and between species

The evolutionary rate should be constant within a species but variable between species

What can a significant p-value in the MK test (i.e. p < 0.05) suggest about the evolution of a gene?

The gene is under positive selection (correct)

The gene is evolving randomly

The gene is under purifying selection

The gene is evolving neutrally

What does it mean if the ratio of non-synonymous to synonymous substitutions within a species is less than the ratio between species in the MK test?

The gene is under purifying selection Signup and view all the answers

What is the purpose of the HKA (Hudson-Kreitman-Aguadé) test?

To compare the level of polymorphism within a species to the level of divergence between species Signup and view all the answers

Which of the following is not a characteristic of the neutral theory of molecular evolution?

Positive selection is the primary driver of molecular evolution Signup and view all the answers

What does an insignificant p-value in the MK test for Positive Selection suggest?

Neutral Evolution Signup and view all the answers

When the rate of evolution is GREATER within species than between species, what could it indicate?

Deleterious alleles in the population Signup and view all the answers

What is the significance of the HKA test in genetics?

To assess the predictions of the Neutral Theory of molecular evolution Signup and view all the answers

In the context of Positive Selection, what does a reduced rate of variation within species due to a sweep suggest?

Loss of Selective Constraint Signup and view all the answers

If the rate of evolution is ~equal within and between species, what evolutionary process does it suggest?

Neutral Evolution Signup and view all the answers

What could be a possible reason for redoing tests on only polymorphisms at medium frequency (>10% in population)?

To minimize the interference of low-frequency deleterious alleles Signup and view all the answers

What is the purpose of the HKA test?

To determine if the observed difference in polymorphism within a species and divergence between species is likely due to neutral evolution or adaptive evolution. Signup and view all the answers

According to the neutral theory of molecular evolution, what is the relationship between the number of segregating sites (S) within a species and the number of divergent sites (D) between species?

S and D are related through the mutation rate and time since divergence between the species. Signup and view all the answers

What does the HKA test assume about the effective population size ($N_e$) and mutation rate ($ u$) across multiple genes?

All genes share the same $N_e$ and $ u$. Signup and view all the answers

If the HKA test rejects the null hypothesis of neutral evolution, what does this indicate?

At least one of the genes has experienced adaptive evolution. Signup and view all the answers

What is the purpose of comparing the level of polymorphism within a species to the level of divergence between species?

To test for the presence of positive selection. Signup and view all the answers

How does the HKA test use the number of segregating sites (S) within a species and the number of divergent sites (D) between species to test for neutral evolution?

It compares the ratio of S to D between two genes to test if the effective population size and mutation rate are the same. Signup and view all the answers

Hudson-Kreitman-Aguade test

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