Molecular evolution - Part 1. Pawan Dhar BII

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1 Molecular evolution - Part 1 Pawan Dhar BII

2 Theodosius Dobzhansky Nothing in biology makes sense except in the light of evolution Age of life on earth: 3.85 billion years Formation of planet: 4.5 billion years

3 How to define life? Notoriously difficult Depends on what we consider to be essential properties of life. Operational definition: Cellular systems that are both autonomously replicating & also subject to Darwanian evolution

4 The logic of life Cell division and differentiation

5 Why cells chose to divide? Numerical increase vs. Structural increase

6 Mathematical basis of cell s choice r 2r Surface area: 2πr Volume: 4/3 πr 3 Volume / Surface area = 0.6 r 2

7 Volume vs. Area of a growing cell Consumption capacity Acquiring ability 1 Increasing radius 2 3 4

8 Background All genes that exist today are presumably derived from a small number of microbes that inhabited earth ~ 3.5 billion yrs ago. Evolution: mutation, gene rearrangement, duplication etc. Aim - to produce molecular diversity

9 Difference between typical prokaryotes and eukaryotes Prokaryotes Dia ~2 microns DNA small, circular No membrane bound organelle RNA and proteins synthesized in same compartment No cytoskeleton Cell cycle ~20 min Eukaryotes Dia ~ 20 microns DNA long, linear, chromosomes Nucleus, mitochondria, chloroplasts RNA - nucleus, Proteins - cytoplasm Cytoskeleton Cell cycle ~ 24 hours

10 What drives Natural selection? Biological selection is accompanied through gene diversity and natural selection Natural selection: viability of phenotypes In-vitro selection: Pre-planned activity test

11 The central dogma (OLD) (NEW)

12 Genome alterations 1/3 Cells do not have specialized mechanisms for creating changes in the structure of their genomes Mechanisms that maintain genome are precise but not perfect

13 Genome alterations 2/3 1 nucleotide pair in a thousand is changed every 200,000 years In a population of 10,000 individuals every possible substitution will have been tried out on about 50 occasions per 1 million years

14 Genome alterations 3/3 DNA sequence alterations can lead to substitutions, duplications, deletions, inversions. The rate of occurrence is shaped by evolutionary forces to provide a balance between change and stability

15 Genome sequence variation and length of time 3 billion years of evolution of 3 billion bases! How to study genomic evolution? Ans: Comparative Genomics

16 Genomic similarity Evolutionary relationship: Humans and Chimps Purifying selection: Humans and mice

17 Humans vs. Chimpanzees Same set and arrangement of 30,000 genes Exception : Chromosome 2 Alu sequences underwent duplication and transposition before divergence of human and chimp lineages 5 million years of divergent history

18 Humans and mouse 100 million years of divergent history Coding sequence much more conserved (synteny) than non-coding sequence Local gene order & chromosome structure divergent ~180 break and rejoin events since H/M shared a common ancestor

19 Reconstructing ancient genomes Ancient genomes can be inferred but NOT directly observed The famous intron-early vs. intronlate controversy No reliable way of solving this controversy

20 Autonomous replication and Darwanian evolution Autonomous replication: continued growth and division, reliant on small molecules and energy, does not depend on the products of preexisting living systems such as protein enzymes. Darwanian evolution requires essential biological aspects of genetic variation and its phenotypic expression as variation in survival and reproduction

21 Designing the protocell Life emerges from the union of two fundamentally different kinds of replicating systems 1. The informational genome 2. Three dimensional structure in which it resides

22 Two main problems Time scale Diversity Artificial molecular evolution efforts must consider both these aspects

23 Manfried Eigen s theory Starts from chemical reaction kinetics and centers on the origin of biological information through replication and mutation. Major outcome: molecular quasispecies and error thresholds

24 Quasispecies 1 of 3 Consists of fittest genotype called the Master sequence and its closely related variants Arise as a result of sufficiently long evolutionary process in presence of mutation rates above a certain threshold.

25 Quasispecies 2 of 3 Increase in mutation rate leads to a decrease in the relative concentration of Master genotype. Beyond threshold of tolerance MS concepts breaks down. Population: non steady state, drifts randomly

26 Quasispecies 3 of 3 The error threshold defines maximal diversity of asexually reproducing populations. E.T. represents maximum variability needed for survival in dynamic environments

27 Can Q.S theory explain evolution? No!! Solution: Combine QS+population migration + genotype--phenotype relationship Strategy for evolution: amplification, diversification and selection

28 Earliest microfossil evidence Bacteria like cells Western Australia (dated 3.5 billion years) Stromatolites - columns of fossilized material formed by bacterial colonies with phototrophs on top and heterotrophs lower down, age assigned 3.5 billion yrs

29 Gene duplication 1 of 3 The main driving force of evolution 1% probability that a gene will undergo duplication every 1 million years Precise mechanism unknown Fate of duplicated gene? Functional divergence Whole genome duplication vs. piecemeal duplication?

30 The DNA-Protein world (2 of 3) Segmental Whole chromosome Tandem copies (Unequal crossing over) Drosophila and C.elegans: hundreds of genes show tandem duplications Can lead to creation of large cluster of genes

31 The DNA-Protein world (3 of 3) On duplication, tandem gene pairs often take on separate gene functions Tandem duplication: Depending on the relative boundaries of UCO may be forced to share common / new regulatory elements Exon shuffling, generation of alternative transcripts and evolution of novel enhancer elements

32 Origin of complexity Mutation, noise and drift Infinite population: negative consequences Finite population: synergistic interaction between noise and drift Emergence of complex networks

33 Evolution of consciousness Four states Unconscious Subconscious Conscious Superconscious

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