‥ Introduction‥ Program

‥ Practice

Phylogenetics

Dr. 王文源

Knowledge needed

‥ Molecular Biology ‥ Bio-Evolution ‥ PC-internet

Field of biology which deals with identifying and understanding the relationships between the many different kinds of life on earth. This includes methods for collecting and analyzing data, as well as interpretations of those results as new biological information.

Phylogenetics=Evolutionary Biology

TaxonomyThe naming, describing, and classification of organisms into different categories according to their characteristics. The biological sciences primarily use the Linnaean classification system for this purpose. It was invented by Carolus Linnaeus(Sweden)

Darwin's theory Evolution by natural selectionCharles Darwin (1809-1882)-"Natural selection"

On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life.

Charles Darwin (1859), On the origin of species, Murray, London.

Lamarck's theory Adaptive nature of evolution

Jean-Baptiste Lamarck (1744-1829)-Adaptation

During its life, an organism may adapt to its environment.

Three important findings of Molecular Biology

1. The discovery of the basic rule of heredity(1865)-Gregor Johann Mendel (1822-1884)

Mendelian law

2. Oswald T. Avery, Colin M. MacLeod, and Maclyn McCarty (1944)-DNA transformation

DNA can carry genetic specificity

3. DNA double helix structure (1953 nature) by James Dewey Watson(1928~) and Francis Harry Compton Crick(1916~)

Explanation of DNA replication and transcriptionSpeeed up development of molecular biology

Related SeqWeb program國家衛生研究院 GCG 巨分子序列分析服務 : http://gcg2.nhri.org.tw/

‥ DNA or Peptide Sequence analysis (eg Beta-lactamase)

‥ BLAST or FASTA Alignments (GenWeb or SeqWeb)

‥ Database search (eg. Reference searching by keyword)

‥ Input interested sequences (Sequence Manager)

‥ Evolutionary Analysis (Grow Tree)

‥ Pileup

‥ Mutation and evolution:1. Base substitution2. The insertion or deletion of single bases3. Inversion of a section of DNA; Recombination (Intragenic inversion; chromosomal inversion)4. Duplication or deletin of a section of the DNA

**The balance between mutation and selection **Deleterious (Lethal) mutation

Genetic variability

UUA, UUG, CUU, CUC, CUA, CUG LEU LEU LEU LEU LEU LEU L L L L L L

Genetic code

Amino acid

UUAUUGCUUCUCCUACUGLEULEULEULEULEULEU TYRCYSPHESERTYR ILEALASERPROTHR

Program download國家衛生研究院分子演化分析 : http://gcg.nhri.org.tw/gcg/phylo

‥Phylip ‥GeneDoc ‥TreeView

s35915

s16553

s23929

s47620

s51044

s17339

a57002

a61156

B-latam

ase

a60448

s16146

a48903

jn0520

s54103

i39695

s41941

s39196

s44094

jh0268

b48899

s33163

i40231

s17287

Rectangular Cladogram Tree

s35915

s16553

s23929

s47620

s51044

s17339

a57002

a61156

B-latam

ase

a60448

s16146

a48903

jn0520

s54103

i39695

s41941

s39196

s44094

jh0268

b48899

s33163

i40231

s17287

Slanted Cladogram Tree

0.1

s35915

s16553

s23929

s47620

s51044

s17339

a57002

a61156

B-latam

ase

a60448

s16146

a48903jn0520

s54103

i39695s41941

s39196

s44094

jh0268

b48899

s33163

i40231

s17287

Phylogram Tree

0.1

B-latamase

a60448

s16146

a48903

jn0520

s54103

i39695s41941

s39196

s44094jh0268

b48899

s33163

i40231

s17287

s17339

a57002

a61156

s35915

s16553

s23929

s47620

s51044

Unrooted Tree

Discussion‥ Phylogenetic just a tool for Biology information‥ Coevolution and ecological relations between the interacting

species (Macroevolution)1. Competition: the presence of each species inhibits the population growth of the other.2. Exploitation: the presence of species A stimulates the growth of B, and the presence of species B inhibits the growth of A. Examples are plant-herbivore, prey-predator, and host-parasite interactions. (A-->B-//-A)3. Mutualism: the presence of each species stimulates the growth of the other.

‥ Science: Open-minded, Continuous, Revised & Created, Not always true or false just evidence

Bioinformatics Internet address

1. 國家衛生研究院巨分子序列分析服務 : http://gcg2.nhri.org.tw/2. 國家衛生研究院分子演化分析 :

http://gcg.nhri.org.tw/gcg/phylo3. 國立陽明大學楊永正教授 POST 系統 :

http://binfo.ym.edu.tw/post/(POST: Problem-Oriented Sequence analysis Tools)

4. 國家高速電腦中心生物資訊學網頁簡介 :http://www2.nchc.gov.tw/~c00chh00/bioinfo.html

5. 台北榮民總醫院教學研究部生物資訊組 :http://www.mre.vghtpe.gov.tw/news/binfor.htm

6. Genbank(NCBI):http://www.ncbi.nlm.nih.gov/genBank/Genbanksearch.html

Nucleotide sequence of the ampicillin resistance gene( beta-lactamase) of Escherichia coli plasmid pBR322 (Genome: 4361 bases; Accession:

J01749 GI:208958)

Sutcliffe,J.G., Nucleotide sequence of the ampicillin resistance gene of Escherichia coli plasmid pBR322. Proc. Natl. Acad. Sci. U.

S.A. 75 (8), 3737-3741 (1978); MEDLINE 79012484