Download Evolution of genes and genomes

Evolution of genes and genomes
Molecular biology
 Tools of molecular biology allow us to see evolution at a smaller scale
 Genomics are the future of molecular biology field
• Genomes of many species are completely sequenced
• Comparative genomics will allow greater insight into evolution
Conservation of structure
Microarrays
 Differential gene expression can be evaluated on a genomic scale
 Contributes more to morphological variation than point substitutions and other
“static” measures
Neutral theory
 Asserts that the great majority of mutations that are fixed are neutral with
respect to fitness
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Fixed by genetic drift
Creates molecular clock
DNA sequencing supports neutral theory
• Synonomous mutations happen more often than replacements
• Rates of substitutions are higher in introns and pseudogenes
• Rate of evolution is higher in genes that are least likely to affect function
Neutral theory
 Most genes are evolving neutrally
 Some genes show adaptive evolution
 Polymorphisms in an allele are transient; a new allele that has arisen by
mutation will either be fixed or lost by genetic drift
 Most change in DNA sequences will be in regions that do not affect fitness
Fibrinopeptides
 Cleavage of fibrinogen during blood coagulation
 Fibrin and fibrinopeptides are produced
• Fibrin is essential
• Fibrinopeptides are discarded
 Which shows a higher rate of gene evolution?
Protein interaction networks
 Interaction of one protein with another
Protein evolution
 Proteins with more interactions evolve more slowly
Purifying selection
 Directional selection for the prevalent homozygous genotype
 New sequence variants are therefore selected against
 Non-synonymous mutations are selected against, synonymous mutations can
accumulate
 The ratio of non-synonymous to synonymous mutations is an index of purifying
selection (ω)
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Normalized by number of sites in each category
What do low values of this ratio indicate?
Histones have highly constrained genes
Positive selection
 Substitution of a mutation that increases fitness
 Accelerates the accumulation of non-synonymous mutations
 If the number of advantageous substitutions exceeds the number of neutral
substitutions (ω >1), then positive selection has acted on the gene
Adaptive convergent evolution
 Lysozyme breaks down bacterial cell walls
 Ruminants and columbine monkeys both have lysozymes to break down
bacterial cell contents of bacteria in their modified foregut or rumen
 Stewart et al. (1987) found that cows and monkeys had same five amino acid
substitutions in lysozyme
Lysozyme evolution
 Langur lysozyme is therefore more similar to cow lysozyme than other
primates
 This gene underwent a rapid change in the ancestral lineage leading to
columbines, associated with the change from a fruit to leaf diet
 Similar rapid evolution in a leaf eating bird
Phylogenetic evidence for molecular convergence in primate, ruminant, and
avian lysozymes
Adaptive evolution of speech
 forkhead box 2 (FOXP2) gene
Adaptive evolution of genomes
 Clark et al. (2003) estimated ω for over 7500 genes from humans and chimps
• Adaptive evolution of 875 genes along human lineage
• Genes encoding for olfactory receptors and amino acid catabolism were
prone to adaptive evolution
• Due to changes in diet and behavior in humans
Diversity of genome structure
 Viral and bacterial genomes minimize unnecessary genes
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Few introns
Use of self splicing
Eukaryotic genomes in comparison contain vast regions of noncoding and
repeat DNA sequences
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Many introns present
Many selfish DNA present
Use of alternative splicing
When did the evolution of introns occur?
 Introns early
• Introns of prokaryotes and eukaryotes are similar
• Introns have been lost over evolutionary time by prokaryotes
 Introns late
• No introns found in basal eukaryotes
• Many introns restricted to specific clades of plants and animals
Phylgenetic distribution of introns
C-value paradox
 Why don’t physiologically more complex organisms have more DNA?
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Organisms vary in their amount of functional to nonfunctional genes
Repetitive sequences and tranposable elements
 Transposable elements are major source of repetitive sequences
 Retroelements encode only for proteins essential for themselves
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• Selfish genes
Fate of retroelements
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Produce daughter elements
Degenerate by mutation and become nonfunctional
Retroelements
 Mutations in retroelements can be used to determine relationships among
copies in a genome and the age of family of retroelements
 Alu elements in primate lineage evolved 50 mya
How do transposable elements affect fitness?
 Usually found between genes and in introns, where they don’t affect function
 Can lead to mutation or chromosome arrangements
 Can lead to adaptive evolution
• Human immune system a result of transposable elements
Diversity of genome sizes and structures
 Lynch and Conery (2003) proposed that:
• Population sizes of bacteria and viruses are large
• Population sizes of eukaryotes are smaller
• Facilitate fixation of nonadaptive traits, such as introns, tranposable
elements, noncoding DNA
How do new genes arise?
 Lateral gene transfer
 Exon shuffling
 Domain accretion
 Retrotranposition
 Gene duplication
Lateral gene transfer
 Horizontal gene transfer
 Transfer of genetic material across different lineages
Phylogenetic evidence for lateral gene transfer – Malic enzyme
Exons and domains
 Division of a gene into exons is related to the division of the protein into
domains
• Domain is a small segment that can fold into a specific three dimensional
structure independent of other domains
Protein domains bind antigens in human immunoglobulin
Domain accretion
 A new gene is formed by the addition of new domain to beginning or end of an
ancestral gene
Evolution and conservation of domains in diverse proteins
Exon shuffling
 New combinations of exons have been produced by nonhomologous
recombination
Origin of new genes via intron-mediated exon shuffling
Origin of a new Drosophila gene, jingwei
 Retrotransposition to form a chimeric gene
Gene duplication
 New genes arise as copies of pre-existing genes
 Gene families
• Show common ancestry
• Have different functions
Gene duplication: Modification of one copy
 Most likely due to uneven crossing over followed by modification of one or
more copies, leading to:
 Gene families
• Such as globins of types α-, β-, ζ-, γ-, εGene evolution within and between species
 Modification through “descent” can occur
• When genes are duplicated and modified within a species over time =
PARALOGOUS
• When genes diverge following speciation = ORTHOLOGOUS
Orthology and paralogy in gene families
How often does duplication occur?
 In vertebrates, >1700 events based on 749 gene families
 Gene families may have blocks of up to 1000 copies (human ribosomal RNA
genes)
 One estimate is 0.01 duplication per gene per million years
Use of age distribution of gene duplication events to infer whole-genome
duplications
Block duplication
Fate of gene duplicates
 Gene conversion
 Neofunctionalization
 Subfunctionalization
Gene conversion
 Sequence from one locus is transferred unidirectionally to other members of
the gene family
• Concerted evolution
Fate of gene duplicates
 Neofunctionalization
• One of the duplicates acquires a new function
 Subfunctinalization
• Each gene becomes specialized for a subset of the functions originally
performed by ancestral single-copy genes