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 )