分子演化 molecular evolution 宣大衛 東華大學生命科學系. molecular evolution an...
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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?
Taxonomy and Systematicsg
分類學 系統生物學
Phylogenetic
Systematics
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.
種系遺傳 系統生物學
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
DNA-based 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)
古生菌細菌
真核生物
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 )