Transcript 分子演化 - 東華大學
分子演化 Molecular Evolution 宣大衛 東華大學生命科學系 Molecular Evolution An historical process that depends on alterations in the structure and organization of genes and gene products Fundamental aspects of cellular life are shared by different organisms and dependent on related genes Small changes in certain genes allow organisms to adapt to new niches Prokaryotic cells Single cell organisms Two main types: bacteria and archaea Relatively simple structure Eukaryotic cells Single cell or multicellular organisms Plants and animals Structurally more complex: organelles, cytoskeleton Modification? 分類學 g 系統生物學 Taxonomy and Systematics Phylogenetic Systematics 種系遺傳 系統生物學 The field of biology that deals with identifying and understanding the evolutionary relationships among the different kinds of life on earth, both living (extant) and dead (extinct). Evolutionary theory states that similarity among individuals or species is attributable to common descent, or inheritance from a common ancestor. Thus, the relationships established by phylogenetic systematics often describe a species' evolutionary history and, hence, its phylogeny (lineages or organisms or their genes. Understanding the Evolutionary Process Genetic Variation: Changes in a gene pool, the genetic make-up of a specific population How Does Genetic Variation Occur? - DNA replication - Mutations The Driving Force of Evolution Selection – genotype, fitness Genetic Drift 漂移 - Fluctuations in the rate of evolutionary processes such as selection, migration, and mutation - Founder Effects - the difference between the gene pool of a population as a whole and that of a newly isolated population of the same species Phylogenetic (Evolutionary) Trees Presenting Evolutionary Relationships Phylogenetic Trees Phylogenetic Trees The Four Steps of Phylogenetic Analysis Alignment - building the data model and extracting a dataset Determining the substitution model consider sequence variation Tree building Tree evaluation Tree Building: Key Features of DNAbased Phylogenetic Trees Comparison of homologs, sequences that have common origins but may or may not have common activity Orthologs - homologs produced by speciation Paralogs - homologs produced by gene duplication within an organism (may have different functions) Xenologs - homologs resulting from the horizontal transfer of a gene between two organisms A typical gene-based phylogenetic tree The tree : 4 external nodes (A, B, C, D) 4 genes 2 internal nodes (e, f) ancestral genes The branch lengths indicate the degree of evolutionary differences between the genes This particular tree is unrooted 3 rooted trees that can be drawn from the unrooted tree shown above, each representing the different evolutionary pathways possible between these four genes Outgroup Outgroup, a gene that is less closely related to A, B, C, and D than these genes are to each other. Outgroups enable the root of the tree to be located and the correct evolutionary pathway to be identified Gene Trees Versus Species Trees - Why Are They Different? It is assumed that a gene tree (molecular data), will be a more accurate than that obtainable by morphological comparisons The two events, mutation and speciation, do not always occur at the same time Molecular clocks require calibration with fossils to determine timing of origin of clades Molecular Clock Hypothesis Nucleotide (or amino acid) substitutions occur at a constant rate The degree of difference between two sequences can be used to assign a date to the time at which their ancestral sequence diverged The rate of molecular change differs among groups of organisms, among genes, and even among different parts of the same gene Sequence Identity Implies Structural Similarity Acipenser milkadoi – largest number of chromosomes of all vertebrate (about 500 mini and macrochromosomes) . Carl Woese, Univ. Illinois Ribosomal RNA Phylogeny and the Primary Lines of Evolutionary Descent Norman Pace, Gary Olson and Carl Woese Cell 45: 325-326 (1986) Unrooted phylogenetic tree based on 16 s-like rRNA sequences. Aligned with 21 rRNA sequences (about 950 nt) 細菌 真核生物 古生菌 Lineage tree of life on earth Common Ancestor ? Mitochondrial DNA and Human Evolution Nature 325(1987)31-36 Allan Wilson, UC Berkeley Why Mitochondrial DNA? Mutation rate ~10 x faster than nuclear genes Inherited maternally and does not recombine Approx 1016 identical Mt DNA molecules within a typical human Conclusions Assuming that mtDNA mutation rate is constant in humans, the sequence divergence of the mtDNAs can be calculated to give all the mtDNA a common ancestor that lived approx. 200,000 years ago (20萬年前) The common ancestor of all human may be from Africa (非洲夏娃) 如何做好 Phylogenic Analysis? Choose informatic regions Make an optimal (500-700 bp) sequence alignment Use different methods to construct the trees Statistical test for phylogenetic trees Methods for Phylogenic Analysis Distance Matrix Method 1. UPGMA (Unweighted Pair Group Method with Arithmetic Average) 2. Neighborhood Joining Method Discrete Characteristic Methods 1. Parsimony Method 2. Maximum Likelihood Method (李文雄院士)