BIOE 109 Summer 2009 Lecture 4- Part I Mutation and genetic variation
1.Mutation 2. Gene Flow 3. Genetic drift 4. Natural selection Four basic processes that can explain evolutionary changes:
Sources of genetic variation 1.Crossing over during meiosis- creates new combinations of alleles on individual chromosomes 2. Independent assortment- creates new combinations chromosomes in the daughter cells
Sources of genetic variation 1.Crossing over during meiosis- creates new combinations of alleles on individual chromosomes 2. Independent assortment- creates new combinations chromosomes in the daughter cells 3. Mutations- create completely new alleles and genes
General classes of mutations
General classes of mutations Point mutations “Copy-number” mutations Chromosomal mutations Genome mutations
Point mutations
Point mutations There are four categories of point mutations:
Point mutations There are four categories of point mutations: 1. transitions (e.g., A G, C T)
Point mutations There are four categories of point mutations: 1. transitions (e.g., A G, C T) 2. transversions (e.g., T A, C G)
Point mutations There are four categories of point mutations: 1. transitions (e.g., A G, C T) 2. transversions (e.g., T A, C G)
Point mutations There are four categories of point mutations: 1. transitions (e.g., A G, C T) 2. transversions (e.g., T A, C G) 3. insertions (e.g., TTTGAC TTTCCGAC)
Point mutations There are four categories of point mutations: 1. transitions (e.g., A G, C T) 2. transversions (e.g., T A, C G) 3. insertions (e.g., TTTGAC TTTCCGAC) 4. deletions (e.g., TTTGAC TTTC)
Point mutations There are four categories of point mutations: 1. transitions (e.g., A G, C T) 2. transversions (e.g., T A, C G) 3. insertions (e.g., TTTGAC TTTCCGAC) 4. deletions (e.g., TTTGAC TTTC) in coding regions, point mutations can involve silent (synonymous) or replacement (nonsynonymous) changes.
Point mutations There are four categories of point mutations: 1. transitions (e.g., A G, C T) 2. transversions (e.g., T A, C G) 3. insertions (e.g., TTTGAC TTTCCGAC) 4. deletions (e.g., TTTGAC TTTC) in coding regions, point mutations can involve silent (synonymous) or replacement (nonsynonymous) changes. in coding regions, insertions/deletions can also cause frameshift mutations.
Loss of function mutations in the cystic fibrosis gene
“Copy-number” mutations
“Copy-number” mutations these mutations change the numbers of genetic elements.
“Copy-number” mutations these mutations change the numbers of genetic elements. gene duplication events create new copies of genes.
“Copy-number” mutations these mutations change the numbers of genetic elements. gene duplication events create new copies of genes. one important mechanism generating duplications is unequal crossing over.
Unequal crossing-over can generate gene duplications
lethal? neutral?
“Copy-number” mutations these mutations change the numbers of genetic elements. gene duplication events create new copies of genes. one mechanism believed responsible is unequal crossing over. over time, this process may lead to the development of multi-gene families.
Chromosome 11 Chromosome 16 and -globin gene families
Timing of expression of globin genes
Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns!
Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns! Example: jingwei in Drosophila yakuba
Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns! Example: jingwei in Drosophila yakuba Alcohol dehydrogenase (Adh) Chromosome 2Chromosome 3
Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns! Example: jingwei in Drosophila yakuba Alcohol dehydrogenase (Adh) Chromosome 2Chromosome 3 mRNA
Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns! Example: jingwei in Drosophila yakuba Alcohol dehydrogenase (Adh) Chromosome 2Chromosome 3 mRNA cDNA
Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns! Example: jingwei in Drosophila yakuba Alcohol dehydrogenase (Adh) Chromosome 2Chromosome 3 mRNA cDNA “jingwei”
Whole-genome data yields data on gene families
“Copy-number” mutations transposable elements (TEs) are common.
“Copy-number” mutations transposable elements (TEs) are common. three major classes of TEs are recognized:
“Copy-number” mutations transposable elements (TEs) are common. three major classes of TEs are recognized: 1. insertion sequences (700 – 2600 bp)
“Copy-number” mutations transposable elements (TEs) are common. three major classes of TEs are recognized: 1. insertion sequences (700 – 2600 bp) 2. transposons (2500 – 7000 bp)
“Copy-number” mutations transposable elements (TEs) are common. three major classes of TEs are recognized: 1. insertion sequences (700 – 2600 bp) 2. transposons (2500 – 7000 bp) 3. retroelements
Chromosomal inversions lock blocks of genes together
Inversions act to suppress crossing-over… inviable
Inversions act to suppress crossing-over… … and can lead to co-adapted gene complexes inviable
Chromosomal inversions in Drosophila pseudoobscura Here is a standard/arrowhead heterozygote:
Here are more inversion heterzygotes:
Chromosomal translocations are also common
Changes in chromosome number are common
in mammals, chromosome numbers range from N = 3 to N = 42.
Changes in chromosome number are common in mammals, chromosome numbers range from N = 3 to N = 42. in insects, the range is from N = 1(some ants) to N = 220 (a butterfly)
Changes in chromosome number are common in mammals, chromosome numbers range from N = 3 to N = 42. in insects, the range is from N = 1(some ants) to N = 220 (a butterfly) karyotypes can evolve rapidly!
Muntiacus reevesi Muntiacus muntjac
Muntiacus reevesi; N = 23 Muntiacus muntjac; N = 4
Genome mutations
polyploidization events cause the entire genome to be duplicated.
Genome mutations polyploidization events cause the entire genome to be duplicated. polyploidy has played a major role in the evolution of plants.
Genome mutations polyploidization events cause the entire genome to be duplicated. polyploidy has played a major role in the evolution of plants. ancient polyploidization events have also occurred in most animal lineages.
Generation of a tetraploid
Where do new genes come from?
An example: the antifreeze glycoprotein (AFGP) gene in the Antarctic fish, Dissostichus mawsoni
Where do new genes come from? An example: the antifreeze glycoprotein (AFGP) gene in the Antarctic fish, Dissostichus mawsoni Reference: Chen et al Proc. Natl. Acad. Sci. USA 94: 3811
Where do new genes come from? An example: the antifreeze glycoprotein (AFGP) gene in the Antarctic fish, Dissostichus mawsoni antifreeze proteins allow these fishes to inhabit subzero sea temperatures.
Where do new genes come from? An example: the antifreeze glycoprotein (AFGP) gene in the Antarctic fish, Dissostichus mawsoni antifreeze proteins allow these fishes to inhabit subzero sea temperatures. act by inhibiting the growth of ice crystals.
Where do new genes come from? An example: the antifreeze glycoprotein (AFGP) gene in the Antarctic fish, Dissostichus mawsoni antifreeze proteins allow these fishes to inhabit subzero sea temperatures. act by inhibiting the growth of ice crystals. the AFGP gene dates to ~10 – 14 million years ago (when Antarctic ocean began to freeze over).
Where do new genes come from? Step 1. Duplication of the pancreatic trypsinogen gene (6 exons long).
Where do new genes come from? Step 1. Duplication of the pancreatic trypsinogen gene (6 exons long). Step 2. Deletion of exons 2 – 5.
see Chen et al Proc. Natl. Acad. Sci. USA 94: 3811
Where do new genes come from? Step 1. Duplication of the pancreatic trypsinogen gene (6 exons long). Step 2. Deletion of exons 2 – 5. Step 3. Expansion of Thr-Ala-Ala triplet 41 times at junction of exon 1.
see Chen et al Proc. Natl. Acad. Sci. USA 94: 3811
Where do new genes come from? Step 1. Duplication of the pancreatic trypsinogen gene (6 exons long). Step 2. Deletion of exons 2 – 5. Step 3. Expansion of Thr-Ala-Ala triplet 41 times at junction of exon 1. Step 4. Expression of AFGP gene in liver, release into blood.
Convergent evolution of an AFGP gene in the arctic cod, Boreogadus saida
the AFGP gene in B. saida also has a Thr-Ala-Ala repeating motif!
Convergent evolution of an AFGP gene in the arctic cod, Boreogadus saida the AFGP gene in B. saida also has a Thr-Ala-Ala repeating motif! appears to have evolved independently because:
Convergent evolution of an AFGP gene in the arctic cod, Boreogadus saida the AFGP gene in B. saida also has a Thr-Ala-Ala repeating motif! appears to have evolved independently because: 1. flanking regions show no homology to trypsinogen
Convergent evolution of an AFGP gene in the arctic cod, Boreogadus saida the AFGP gene in B. saida also has a Thr-Ala-Ala repeating motif! appears to have evolved independently because: 1. flanking regions show no homology to trypsinogen 2. different number and locations of introns
Convergent evolution of an AFGP gene in the arctic cod, Boreogadus saida the AFGP gene in B. saida also has a Thr-Ala-Ala repeating motif! appears to have evolved independently because: 1. flanking regions show no homology to trypsinogen 2. different number and locations of introns 3. codons used in repeating unit are different