Adaptive Protein Divergence and MK Test

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Questions and Answers

What is the significance of the HERC2 rs12913832*C single nucleotide polymorphism (SNP)?

It indicates a gene duplication event.

It has no known phenotypic associations.

It is associated with increased skin pigmentation.

It is linked to blue eye color. (correct)

Which statement accurately describes the evolutionary history of light skin pigmentation in European populations?

The adaptive spread of light skin pigmentation was complete by the Mesolithic.

Light skin pigmentation evolved in parallel with blue eye color.

The evolution of light skin is a recently developed trait. (correct)

Alleles associated with light/blue eye color spread after changes in skin pigmentation.

What might be one consequence of gene duplications and deletions?

They have no impact on human phenotypes.

They can lead to dosage effects and gene disruption. (correct)

They are always beneficial to the organism.

They increase the overall genetic diversity of a population.

What historical trait combination is unique and no longer present in contemporary European populations?

Dark skin with light eyes. Signup and view all the answers

What is one of the theories for the evolution of lighter skin at high latitudes?

Selection based on Vitamin D synthesis due to reduced UV energy. Signup and view all the answers

Which of the following conditions may be associated with copy number variants?

Color-blindness and autism. Signup and view all the answers

How does folate sensitivity relate to skin pigmentation in varying latitudes?

More pigment protects against folate depletion at low latitudes. Signup and view all the answers

In the context of mammalian evolution, what is the relevance of gene duplications?

They allow for evolution of gene families. Signup and view all the answers

What role does the SLC24A5 gene play in pigmentation?

It affects pigmentation in both humans and zebrafish. Signup and view all the answers

What type of homology is associated with speciation events?

Orthology. Signup and view all the answers

What is a consequence of having darker skin at higher latitudes?

Ineffective Vitamin D synthesis leading to health issues. Signup and view all the answers

Which process is NOT typically a result of unequal crossing-over?

Specific SNP formation. Signup and view all the answers

What evolutionary adaptation is associated with populations that have lower constitutive skin pigmentation?

Increased tanning ability due to seasonal high UV. Signup and view all the answers

Which factor is NOT associated with the variation of skin color among human populations?

Hormonal changes related to climate. Signup and view all the answers

Which of the following statements about racial pigmentation differences is true?

Latitudinal influence plays a significant role in pigmentation variation. Signup and view all the answers

What historical factor is suggested to influence allelic frequency in pigmentation?

Migration patterns and isolation of populations. Signup and view all the answers

What role does the SLC24A5 allele play in relation to skin pigmentation among Europeans and Asians?

It is not present at high frequency in light-skinned Asian populations. Signup and view all the answers

Which gene makes a significant contribution to light skin in Chinese populations?

OCA2 Signup and view all the answers

What does the evidence suggest about the evolution of lighter pigmentation in Europeans and Asians?

A significant amount of lighter pigmentation evolved independently in each group. Signup and view all the answers

Which of the following statements is supported by the information on pigmentation variation?

OCA2 is correlated with pigmentation variation within the Chinese population. Signup and view all the answers

How is the concept of convergent evolution illustrated in terms of skin pigmentation?

Distinct genetic mechanisms lead to similar skin pigmentation traits in different groups. Signup and view all the answers

Which statement correctly describes the genetic architecture in the context of human pigmentation?

There are both derived and ancestral pigmentation alleles in ancient populations. Signup and view all the answers

What can be inferred about the allelic frequency of light skin alleles?

Some alleles are more frequent in certain geographical populations than others. Signup and view all the answers

Which evolutionary perspective is relevant when analyzing the genetic basis of human skin color?

Natural selection plays a significant role in the evolution of pigmentation. Signup and view all the answers

Study Notes

Codan Usage and Adaptive Protein Divergence

Codan usage is determined mostly by mutation bias.
More sensitive methods exist for detecting adaptive protein divergence than dN/dS, such as the McDonald-Kreitman (MK) test.

The McDonald-Kreitman (MK) Test

This test assesses neutral evolution versus adaptive evolution.
Under the null hypothesis (neutral evolution), polymorphism and divergence are from genetic drift.
Rapidly evolving proteins show high polymorphism levels within species compared to fixed variants.
Compares protein polymorphism/fixed variants to synonymous variants.
Effective only if there are many selectively fixed amino acids and multiple variants within a gene.

Logic of the MK Test

Under neutrality, the ratio of polymorphic to fixed nonsynonymous variants equals the ratio of polymorphic to fixed synonymous variants.
An example dataset following neutrality will have a ratio of 5/10 = 10/20 = 0.5.

Datasets Incompatible with Neutral Protein Variation

Datasets showing disparities between the ratios of polymorphic to fixed nonsynonymous and synonymous variants indicate adaptive evolution.
A significant Fisher's exact test (G-test) p-value (<10^-5) suggests the data is incompatible with neutral evolution.

Effects of Directional Selection on Linked Genomic Regions

Polymorphism is positively correlated with recombination rate.
Directional selection on linked genomic regions influences protein divergence.
In mammals, the effects of directional selection on mammalian genomes are smaller than effects on fly genomes.

9 Polymorphism = ↑ Mutation Rate = ↑ Divergence

Increased polymorphism often correlates with higher mutation rates and greater divergence.

Hitchhiking Effect (Selective Sweep)

The hitchhiking effect allows mutations to spread alongside beneficial mutations.
The spread of beneficial mutations can lead to the reduction in variation within a genome.
A dataset incompatible with neutral protein variation can be due to selective sweeps driving changes in allele frequency.

No Recombination

No recombination near a gene can result in the fixation of the gene near by due to strong selection pressure.
Recombination can reduce the strength of natural selection and lead to more diversity.

What Fraction of Protein Divergence is due to Directional Selection?

In D. simulans, 20% of genes evidence adaptive protein evolution
30-50% of amino-acid fixations are due to directional selection, not neutral (drift) events.

Current Evidence Suggests...

Adaptive evolution of non-coding DNA is common in flies.
Effects of directional selection on mammalian genomes are smaller than effects on fly genomes.

Evolution of Lactase Persistence

Data indicates that the evolution of lactase persistence is comparatively recent.
The presence of specific genetic variants (alleles) correlates with the ability to digest lactose.
The ability to digest lactose is not present in all humans.

Map of Recent Positive Selection in the Human Genome

Various genomic regions show evidence of recent positive selection.

Adaptation to Low Oxygen Pressure

Tibetans have adapted to low oxygen pressure by recent selection for specific genetic variants.

Geographic Location and Genetic Affinities

The geographic location of individuals and their genetic affinities are related to the presence or absence of specific alleles

Evolution of Human Skin Pigmentation

The development of darker skin is thought to be a result of complex selection pressures, including the need to maintain folate levels and regulation of vitamin D synthesis in locations with lower UV radiation.

Pigmentation Alleles

Certain alleles (e.g., SLC24A5) correlated are associated with differences in pigmentation in various populations

De Novo Gene Evolution

Genes can originate from non-genic DNA regions through cis-acting regulatory mutations.

Genome Size Variation

Genome size variation is often unexplained by gene content but is affected by repetitive DNA.

Mammalian HemoGlobin

Mammalian hemoglobin subfamilies arose by duplication.

Two Types of Homologies

Orthology (speciation)- related by gene duplication events.
Paralogy (duplication): related by ancestral duplicated genes, and diverged.

Gene Duplications

Duplications can result in deleterious effects from gene dosage but can also create new functions.

Anti-Freeze Protein Evolution

Anti-freeze proteins in antarctic fish result from non-coding regions of a digestive enzyme.
These proteins are derived from an existing protein, which subsequently acquires a new function.

Homologous Sequence Identification

Homologous sequences that are present in all species, but exhibit expression and open reading frame in one species, represent recently evolved genes.

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Description

This quiz explores the principles of codon usage and adaptive protein divergence, focusing on the McDonald-Kreitman (MK) test. It examines how the MK test differentiates between neutral and adaptive evolution by comparing polymorphism and fixation rates. Test your understanding of these important concepts in evolutionary biology!