1. Duplication, rearrangement, and mutation of DNA contribute to genome evolution
Chapter 21, Section 5

2. Overview
The basis of change at the genomic level is mutation, which underlies much of genome evolution.
Genome Size
The earliest forms of life likely had a minimal number of genes, including only those necessary for survival and reproduction.
The size of genomes has increased over evolutionary time, with the extra genetic material providing raw material for gene diversification.
E.coli (one circular chromosome)genome and a cat genome (multiple chromosomes).

3. Duplication of Entire Chromosome Sets
Accidents in meiosis can lead to one or more extra sets of chromosomes, a condition known as polyploidy.
One set of genes can provide essential functions for the organism.
The genes in one or more extra set can diverges by accumulating mutations.
As long as one copy of an essential gene is expressed, the divergence of another copy can lead to its encoded protein acting in a novel way, thereby changing the organism’s phenotype.
May result in branching off of a new species.
Common in flowering plants.

4. Alterations of Chromosome Structure
Human chromosome 2
Chimpanzee chromosomes
Telomere sequences
Alterations of Chromosome Structure
Centromere sequences
Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs.
Following the divergence of humans and chimpanzees from a common ancestor, two ancestral chromosomes fused in the human line.
The banding patterns is stained chromosomes suggested that the ancestral versions of current chimp chromosome 12 and 13 fused end to end, forming chromosome 2 in an ancestor of the human lineage.
Telomere-like sequences 12
Centromere-like sequences 13
(a) Human and chimpanzee chromosomes

5. Human chromosome 16 Mouse chromosomes 7 8 16 17
For human chromosome 16, a comparison revealed that large blocks of genes on this chromosome are found on four mouse chromosomes.
This observation suggests that the gens in each block stayed together during the evolution of the mouse and human lineages. 7 8 16 17
(b) Human and mouse chromosomes

6. Comparative analysis between chromosomes of humans and seven mammalian species paints a hypothetical chromosomal evolutionary history.
Duplications and inversions result from mistakes during meiotic recombination.
The rate of duplications and inversions seems to have accelerated about 100 million years ago.
This coincides with when large dinosaurs went extinct and mammals diversified.
Chromosomal rearrangements are thought to contribute to the generation of new species.
Some of the recombination “hot spots” associated with chromosomal rearrangement are also locations that are associated with diseases.

7. Duplication and Divergence of Gene-Sized Regions of DNA
Nonsister chromatids
Transposable element
Gene
Duplication and Divergence of Gene-Sized Regions of DNA
Incorrect pairing of two homologs during meiosis
Crossover point
Unequal crossing over during prophase I of meiosis can result in one chromosome with a deletion and another with a duplication of a particular region.
Transposable elements can provide sites for crossover between nonsister chromatids.
Slippage can occur during DNA replication, such that the template shifts with respect to the new complementary strand, and a part of the template strand is either skipped by the replication machinery or used twice.
and

8. Evolution of Genes with Related Functions: The Human Globin Genes
The genes encoding the various globin proteins evolved from one common ancestral globin gene, which duplicated and diverged about 450–500 million years ago.
Each of these genes were later duplicated several times, and the copies then diverged from each other in sequence, yielding the current family members.
After the duplication events, differences between the genes in the globin family arose from the accumulation of mutations.
Many mutations had adverse effects or no effect.
Few mutations must have altered the function of the protein product in a way that was advantageous to the organism at a particular life stage without substantially changing the protein’s oxygen carrying function.

9. The similarity in the amino acid sequences of the various globin proteins supports this model of gene duplication and mutation.

10. Evolution of Genes with Novel Functions
The copies of some duplicated genes have diverged so much in evolution that the functions of their encoded proteins are now very different.
For example the lysozyme gene was duplicated and evolved into the gene that encodes α-lactalbumin in mammals.
Lysozyme is an enzyme that helps protect mammals and birds (animals) against bacterial infection.
α-lactalbumin is a nonenzymatic protein that plays a role in milk production in mammals.
Some time after the lineages leading to mammals and birds had separated, the lysozyme gene was duplicated in the mammalian lineage, but not in the avian lineage.
Lysozyme
α-lactalbumin

11. Rearrangements of Parts of Genes: Exon Duplication and Exon Shuffling
Proteins often have a molecular architecture consisting of discrete structural and functional regions called domains.
Different exons code for the different domains of a protein.
Errors in meiosis can result in an exon being duplicated on one chromosome and deleted from the homologous chromosome.
The gene with the duplicated exon would code for a protein containing a second copy of the encoded domain.
This change in the protein’s structure could augment its function.
Protein-coding genes that have multiple copies of related exons could have arose by duplication and then diverged.
Example: collagen

12. Exon Shuffling
In exon shuffling, errors in meiotic recombination lead to some mixing and matching of exons, either within a gene or between two nonallelic genes.
Exon shuffling could lead to new proteins with novel combinations of functions.

13. How Transposable Elements Contribute to Genome Evolution
Multiple copies of similar transposable elements may facilitate recombination, or crossing over, between different chromosomes.
The movement of transposable elements can have a variety of consequences:
Insertion of transposable elements within a protein-coding sequence may block protein production.
Insertion of transposable elements within a regulatory sequence may increase or decrease protein production.
Transposable elements may carry a gene or groups of genes to a new position.
Transposable elements may also create new sites for alternative splicing in an RNA transcript.
In all cases, changes are usually detrimental but may on occasion prove advantageous to an organism.
To be heritable, these changes must occur in germ cells.

14. Concept Check
Describe three examples or errors in cellular processes that lead to DNA duplications.
Explain how multiple exons arise in the ancestral EGF and fibronectin genes.
What are three ways that transposable elements are thought to contribute to genome evolution?
If meiosis is faulty, two copies of the entire genome can end up in a single cell. Errors in crossing over during meiosis can lead to one segment being duplicated while another is deleted. During DNA replication, slippage backward along the template strand can result in segment duplication.
For either gene, a mistake in crossing over during meiosis could have occurred between the two copies of that gene, such that one ended up with a duplicated exon. This could have happened several times, resulting in the multiple copies of a particular exon in each gene.
Multiple copies of similar transposable elements may facilitate recombination, or crossing over, between different chromosomes. Insertion of transposable elements within a protein-coding sequence may block protein production. Insertion of transposable elements within a regulatory sequence may increase or decrease protein production. Transposable elements may carry a gene or groups of genes to a new position, which can lead to dispersion of genes and in some cases different patterns of expression. Transport of an exon during transposition and its insertion into a gene may add a new functional domain to the originally encoded protein, a type of exon shuffling.