* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Evolution of genes and genomes
Neuronal ceroid lipofuscinosis wikipedia , lookup
Copy-number variation wikipedia , lookup
Human genome wikipedia , lookup
Epigenetics of neurodegenerative diseases wikipedia , lookup
Oncogenomics wikipedia , lookup
Transposable element wikipedia , lookup
Pathogenomics wikipedia , lookup
Public health genomics wikipedia , lookup
Genomic imprinting wikipedia , lookup
Gene therapy wikipedia , lookup
Ridge (biology) wikipedia , lookup
Genetic engineering wikipedia , lookup
Non-coding DNA wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Biology and consumer behaviour wikipedia , lookup
Population genetics wikipedia , lookup
Minimal genome wikipedia , lookup
Gene desert wikipedia , lookup
Adaptive evolution in the human genome wikipedia , lookup
Gene nomenclature wikipedia , lookup
Epigenetics of human development wikipedia , lookup
Nutriepigenomics wikipedia , lookup
The Selfish Gene wikipedia , lookup
History of genetic engineering wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
Gene expression programming wikipedia , lookup
Point mutation wikipedia , lookup
Genome (book) wikipedia , lookup
Site-specific recombinase technology wikipedia , lookup
Gene expression profiling wikipedia , lookup
Helitron (biology) wikipedia , lookup
Genome evolution wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
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 • • • 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) • • 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 • • Few introns Use of self splicing Eukaryotic genomes in comparison contain vast regions of noncoding and repeat DNA sequences • • • 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? • 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 • Selfish genes Fate of retroelements • • 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