1.  Introduction  Program  Practice Phylogenetics Dr. 王文源

2. Knowledge needed  Molecular Biology  Bio-Evolution  PC-internet

3. 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

4. Taxonomy The 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)

5. Darwin's theory Evolution by natural selection Charles 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.

6. Lamarck's theory Adaptive nature of evolution Jean-Baptiste Lamarck (1744-1829)-Adaptation During its life, an organism may adapt to its environment.

7. 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 transcription  Speeed up development of molecular biology

8. 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

9.  Mutation and evolution: 1. Base substitution 2. The insertion or deletion of single bases 3. 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

10. UUA, UUG, CUU, CUC, CUA, CUG LEU LEU LEU LEU LEU LEU L L L L L L Genetic code Amino acid UUAUUGCUUCUCCUACUG LEULEULEULEULEULEU TYRCYSPHESERTYR ILEALASERPROTHR

13. Program download 國家衛生研究院分子演化分析 : http://gcg.nhri.org.tw/gcg/phylohttp://gcg.nhri.org.tw/gcg/phylo  Phylip  GeneDoc  TreeView

15. s35915s16553 s23929 s47620s51044s17339 a57002a61156 B-latamase a60448 s16146 a48903 jn0520 s54103 i39695 s41941s39196s44094 jh0268 b48899 s33163 i40231 s17287 Rectangular Cladogram Tree

16. s35915s16553 s23929 s47620s51044s17339 a57002a61156 B-latamase a60448 s16146 a48903 jn0520 s54103 i39695 s41941s39196s44094 jh0268 b48899 s33163 i40231 s17287 Slanted Cladogram Tree

17. 0.1 s35915 s16553 s23929 s47620 s51044 s17339 a57002a61156 B-latamase a60448 s16146 a48903 jn0520 s54103 i39695 s41941 s39196 s44094 jh0268 b48899 s33163 i40231 s17287 Phylogram Tree

18. 0.1 B-latamase a60448 s16146 a48903 jn0520 s54103 i39695 s41941 s39196 s44094 jh0268 b48899 s33163 i40231 s17287 s17339 a57002 a61156 s35915 s16553 s23929 s47620 s51044 Unrooted Tree

20. 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

21. 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/phylo 3. 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

22. 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