Genome Evolution Lec 13

Question 1

What are some factors that contribute to the C-value paradox?

Answer 1

■Large proportions of non-coding DNA: A significant portion of eukaryotic genomes consists of non-coding sequences, such as introns and intergenic regions.

■Whole-genome duplications (WGDs): Duplication of the entire genome can lead to a substantial increase in DNA content.

Question 1

What is the C-value paradox?

Answer 1

Refers to the observation that genome size does not correlate with organismal complexity.

Some organisms with relatively simple body plans have much larger genomes than more complex organisms.

Question 2

What are the two main types of transposable elements (TEs)?

Answer 2

■DNA-based transposons: These TEs move by a “cut-and-paste” mechanism, using the enzyme transposase.

■RNA transposons or retrotransposons: These TEs move by a “copy-and-paste” mechanism, involving an RNA intermediate.

Question 3

How can transposable elements affect phenotypes?

Answer 3

■Neutral or Deleterious: Most TE insertions have no effect or are slightly harmful.

■Gene Disruption: TEs can insert into coding regions, disrupting gene function and potentially leading to disease.

■Regulatory Changes: TEs can alter gene regulation by providing new enhancer or promoter sequences.

Question 4

What is the dN/dS ratio and what does it tell us about selection?

Answer 4

The dN/dS ratio compares the rate of nonsynonymous substitutions (dN), which change the amino acid sequence, to the rate of synonymous substitutions (dS), which do not change the amino acid sequence.

■dN/dS < 1: Purifying selection (selection against change)

■dN/dS = 1: Neutral evolution (drift)

■dN/dS > 1: Positive selection (selection for change

Question 4

How do host genomes defend against TEs?

Answer 4

DNA methylation: This epigenetic modification can silence TEs by preventing their transcription.
■Mutation: Mutations can accumulate in TEs over time, rendering them inactive.

Question 5

What is the relationship between effective population size (Ne) and the power of selection versus drift?

Answer 5

■Large Ne: Selection is more effective, and beneficial mutations are more likely to fix.
■Small Ne: Drift is more powerful, and slightly deleterious mutations may fix. This can make adaptation more difficult.

Question 6

How do chromosomal inversions contribute to evolution?

Answer 6

Chromosomal inversions are rearrangements that flip a segment of a chromosome. They can:

■Reduce recombination: Genes within an inversion are inherited together, which can maintain beneficial combinations of alleles.

■Spread by drift or selection: Inversions can increase in frequency due to random chance or if they provide a selective advantage.

■Contribute to speciation: Inversions can contribute to reproductive isolation between populations, leading to the formation of new species.

Question 7

What is the role of gene duplication in evolution?

Answer 7

Gene duplication creates extra copies of genes, providing raw material for evolutionary innovation. The duplicated genes can have various fates:

■Conservation: Both copies remain functional and retain their original function. This can increase gene dosage, as with the AMY1 gene in humans.

■Neofunctionalization: One copy acquires a new function, while the other retains the original function. An example is the RNASE1B gene in leaf-eating monkeys.
■
Subfunctionalization: Both copies specialize in performing a subset of the original function. Mammalian hemoglobin, with fetal and adult forms, exemplifies this.

■Gene Loss: One copy may become nonfunctional (a pseudogene) and eventually be lost.

Question 8

What is whole-genome duplication (WGD), and what are its evolutionary consequences?

Answer 8

WGD is the duplication of the entire genome, resulting in polyploidy. WGDs have had major impacts on the evolution of plants and some animal lineages. They can:

■Provide raw material for diversification: Duplicated genes can evolve new functions, leading to increased complexity.

■Affect regulatory networks: WGDs can disrupt existing regulatory networks and create new ones.

■Contribute to speciation: Polyploidy can lead to reproductive isolation from diploid ancestors.

Question 9

What is a genome?

Answer 9

A genome is the complete set of genetic material in an organism. It is an ordered series of nucleotide bases (A, T, C, G) encoded in each cell, containing both coding and non-coding regions. The genome provides instructions for the development of phenotypes and serves as the molecular basis of adaptation.

Question 10

What is the C-Value Paradox?

Answer 10

The C-Value Paradox describes the lack of correlation between genome size and organismal complexity. It highlights that genome size does not uniformly increase with morphological complexity and that organisms with similar gene numbers can have vast differences in genome size

Question 11

What are the factors contributing to the C-Value Paradox?

Answer 11

■Large proportions of non-coding DNA: Eukaryotic genomes contain a large percentage of non-coding DNA, including introns within genes and intergenic regions between genes.
■Whole-genome duplications (WGDs): Duplication of the entire genome can significantly increase DNA content without necessarily increasing gene number.
■Mobile genetic elements: These elements can replicate and insert themselves into various parts of the genome, increasing its size.

Question 12

How does genome architecture impact phenotypes?

Answer 12

Genome architecture, including the size, organization, and content of the genome, can influence phenotypes in several ways:

■Gene regulation: The arrangement of regulatory elements and non-coding regions can affect gene expression patterns, leading to phenotypic variations.

■Chromosomal rearrangements: Inversions, translocations, and other structural changes can alter gene expression and linkage, impacting phenotypes.

■Mobile element insertions: The insertion of transposable elements can disrupt genes, alter regulatory regions, or create new genetic variations, leading to phenotypic changes.

■Gene duplication and loss: Duplication of genes can provide new genetic material for evolutionary change, while gene loss can simplify genomes and eliminate redundant functions. These changes can influence the evolution of new traits or the loss of existing ones

Question 13

What are the sources of new genes?

Answer 13

Horizontal Gene Transfer (HGT): The transfer of genetic material between organisms that are not directly related. This is common in bacteria and can occur in eukaryotes, as seen in the example of red aphids acquiring a carotenoid desaturase gene from fungi.

■Gene Duplication: The creation of an extra copy of a gene. This can occur through various mechanisms, including crossing over errors, replication slippage, and retrotransposition.

■Whole Genome Duplication (WGD): The duplication of the entire genome, leading to polyploidy. This can be caused by errors during meiosis or hybridization events.

Question 14

What are the possible fates of duplicated genes?

Answer 14

■Conservation: Both copies retain their original function, potentially increasing gene dosage (e.g., AMY1 gene in humans).
■Neofunctionalization: One copy acquires a new function while the other retains the original function (e.g., RNASE1B gene in leaf-eating monkeys).
■Subfunctionalization: Both copies specialize, each performing a subset of the original function (e.g., fetal and adult hemoglobin in mammals).
■Gene Loss: One copy becomes nonfunctional (a pseudogene) and may eventually be lost from the genome.

Question 15

What are transposable elements (TEs)?

Answer 15

TEs are mobile genetic elements that can move and replicate within a genome. They are often referred to as “jumping genes”. There are two main types:

■DNA-based transposons: These TEs move through a “cut-and-paste” mechanism using the enzyme transposase.
■RNA transposons or retrotransposons: These TEs use a “copy-and-paste” mechanism involving an RNA intermediate.

Question 16

What are the phenotypic effects of TEs?

Answer 16

TEs can have a range of phenotypic effects, from neutral to deleterious:

■Neutral: Insertions into intergenic regions might not affect phenotype.

■Deleterious: Insertions into coding regions can disrupt gene function and cause disease.

■Beneficial: In some cases, TEs can contribute to phenotypic novelty by altering gene regulation or creating new genetic variations. Examples include the Rider retrotransposon in tomatoes and the relationship between TE insertions and intron evolution.

Question 17

What defense mechanisms do host genomes employ against TEs?

Answer 17

DNA Methylation: This epigenetic modification can silence TEs by inhibiting their transcription.

■Mutation: Mutations can accumulate in TEs, rendering them inactive over time.

Question 18

What is the dN/dS ratio, and how does it relate to selection pressure on coding regions?

Answer 18

The dN/dS ratio compares the rate of non-synonymous substitutions (dN) to the rate of synonymous substitutions (dS). It can be used to infer the type of selection acting on a protein-coding gene:
■
dN/dS < 1: Indicates purifying selection, where deleterious mutations are removed, and the protein sequence is conserved.
■
dN/dS = 1: Suggests neutral evolution, where mutations are not selectively advantageous or disadvantageous and accumulate by drift.
■
dN/dS > 1: Implies positive selection, where advantageous mutations are favored, leading to rapid changes in the protein sequence.

Question 19

How does effective population size (Ne) impact the balance between selection and drift?

Answer 19

Effective population size plays a crucial role in determining the relative strength of selection and drift:

■Large Ne: Selection is more efficient, and beneficial mutations are more likely to fix while deleterious mutations are purged. This promotes adaptation.

■Small Ne: Drift becomes more influential, allowing slightly deleterious mutations to fix and hindering the fixation of beneficial mutations. This can limit adaptation. For example, fruit flies have larger Ne and show more signs of adaptation than humans, which have smaller Ne and more evidence of drift.