Molecular evolution L7-8

Question 1

Give examples of how prokaryotic and eukaryotic genomes differ.

Answer 1

Prokaryotes have circular DNA and eukaryotes have linear DNA.

Eukaryotes have larger less effective genomes because they contain a lot of introns, transposable elements and repetitive DNA. Prokaryotic DNA are mostly composed of protein-coding genes.

Eukaryotes have mitochondrial DNA.

Eukaryotes pack their DNA around histones in the nucleus and prokaryotes supercoils their DNA in the cytosol.

Question 2

What is the C-value paradox?

Answer 2

Larger genome does not give more genes in eukaryotes.

I.e. genome size is not a good measure of complexity since we lack correlation between genome size and number of genes.

Question 3

Why is selection not as strong on eukaryotes as on prokaryotes?

Answer 3

Becuase eukaryotes have less part of the genome coding for proteins. So the parts of the genome with high constraint are fewer. Eukaryotes are therefore more affected by drift.

Question 4

What is genome synteny? what can be the reason for lack of synteny?

Answer 4

We have genome synteny if genes are on the same chromosome for different species.

Lack of synteny is usually the cause of translocations.

Question 5

What is genome collinearity? What types of mutations can change it?

Answer 5

The genes occur in the same order between different species.

Inversions, duplications, deletions, insertions.

Question 6

What is the utility of synteny inference?

Answer 6

• The relative order of genes in one species can provide clues about the presence and function of genes in another species.
• The order of genes in annotated genomes of one species can help discover genes by homology to another species that were missed by gene-finding algorithms.
• Can help detect segmental duplications across species.

Question 7

What is the cause of there being less G-C content?

Answer 7

There is a mutational bias towards G-C –> A-T.

There is however a selection that works against this bias called the fixation bias that works so that G-C alleles gets fixated over A-T alleles.

The evolution of G-C content is the result of the balance between these two.

Question 8

What is horizontal gene transfer?

Answer 8

We generally assume vertical transmission of DNA from parents to offspring but DNA my also be transferred horizontally between lineages.

This is most common in prokaryotes but i can occur in eukaryotes too however very rarely.

Question 9

What advantages does horizontal gene transfer give to bacteria?

Answer 9

• evolution
• survival
  -adaptation to different environments
• acquisition of antibiotic resistence
• acquisition of virulence.

Question 10

How can we detect horizontal gene transfer?

Answer 10

It leads to inconsistencies between gene trees and species trees.

Question 11

Why do we see a general increase in genome size and gene number as one progresses from more basal organisms to derived ones?

Answer 11

Largely because of gene duplications. This is because they have a very high birth rate. The duplication rate is 10.000x larger than the base substitution rate.

Question 12

If duplications contribute to evolution then why does not trisomies?

Answer 12

Because trisomies generally decrease fitness so they’re a dead end for evolution.

Question 13

What is the mechanism of a gene duplication? What are the different types of duplications?

Answer 13

Replication errors.

Partial gene duplication
Complete gene duplication
Segmental duplication
Complete chromosomal duplication (aneuploidy).

Question 14

What is a gene family?

Answer 14

paralogs and orthologs which are derived from a common ancestral gene. These are usually clustered together on the same chromosome.

Question 15

What are the possible fates of a duplicated gene?

Answer 15

One of the copies has no function so the function remains the same - Nonfunctionalization.

Double the function of the gene - Conservation.

Both copies loose some function and they both together maintain the function - Subfunctionalization.

One copy has the original function and the other gets a new function. Neofunctionalization.

Question 16

What is convergent evolution?

Answer 16

Two species in different environments can evolve the same characteristics and traits without it evolving from a common ancestor but instead from gene duplications or deletions.

Question 17

What is poliploidization? Can it happen in humans?

Answer 17

Duplication of the whole genome. This is common in plants.

If sex is determined by X, Y chromosomes then polyploidy is not possible because of gene dosage issues.

Question 18

What is allopolyploids?

Answer 18

When two species hybridize and give polyploidy.

Question 19

What is diploidization?

Answer 19

Evolutionary process whereby a tetraploid species decays to become a diploid with twice as many distinct chromosomes.

Question 20

What is a transposable element?

Answer 20

A nucleotide sequence that can change its position (transpose) within a genome, sometimes creating or reversing mutations and altering the cell’s genetic identity and genome size.

TEs take up a large fraction of the eukaryotic genome.

Their only reason for existing is to make more copies of themselves.

They encode for their own enzymes that help them jump.

Question 21

What are the two different types of TEs?

Answer 21

retrotransposons (copy and paste)
DNA transposons (cut and paste)

Question 22

Explain the difference between retrotransposons and DNA transposons.

Answer 22

They differ in how they make new copies of themselves.

retrotransposons duplicates themselves and then moves to a new location.

DNA transposons moves to a new location in front of the replication fork.

Question 23

How can TEs reduce fitness?

Answer 23

TEs impose a huge fitness cost because they jump into the middle of genes and disrupts their function.

Very rarely this can cause beneficial mutations.

They can also have an impact when they insert themselves into non-coding regions near genes and alters their expressions.