Phylogenetic tree in microbial taxonomy
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Phylogenetic trees show evolutionary relationships between organisms or species. They can be rooted, with a starting common ancestor, or unrooted, showing only relatedness. Trees are constructed through distance-based methods, which calculate dissimilarity between sequences, or character-based methods like maximum parsimony, which finds the tree with the fewest evolutionary changes, and maximum likelihood, which finds the tree with the highest probability based on character data. Phylogenetic trees are significant for studying evolutionary histories, tracing infectious diseases, and discovering new species.
Phylogenetic tree in microbial taxonomy
- 2. content 1. Phylogeny 2. Phylogenetic tree : definition. 3. Origin of phylogenetic tree. 4. Types of phylogenetic tree. 5. Construction of phylogenetic tree. 6.significance of phylogenetic tree. KKR1116 2
- 3. PHYLOGENY Phylogeny is the study of the history of the evolution of a organism species or group. OR Study of evolutionary relationships between species or organism. KKR1116 3
- 4. PHYLOGENETICTREE Diagrammatic representation. It shows the evolution of the organisms or species. It shows the relationship between the species or the group of organism. Also called “Tree of life” or “dendrogram”. Referred as two dimensional graph as it represents the evolutionary relationship between an organism from various other organism. Derived from the ancient Greek word, which refers to race,origin,or lineage. KKR1116 4
- 5. origin/ historyof phylogenetictree. Carl Woese’s Classification KKR1116 5
- 6. Carl Woese’s Classification is also known as the Three-domain system. This classification system divides the life forms into three domains and six kingdoms, that is why it also called the Six Kingdoms and Three Domains Classification. The three domains are archaea, bacteria, eukaryote, and six kingdoms are Archaebacteria (ancient bacteria), Eubacteria (true bacteria), Protista, Fungi, Plantae, Animalia. KKR1116 6
- 7. Woese classified them based on their differences in the 16S ribosomal RNA (rRNA) structure. Carl Woese used the rRNA as an “Evolutionary Chronometer” – an evolutionary time clock. KKR1116 7
- 8. KKR1116 8
- 9. TYPES OF PHYLOGENETIC TREE •ROOTED TREE •UNROOTED TREE KKR1116 9
- 10. ROOTEDTREE • A rooted phylogenetic tree is a type of phylogenetic tree that describes the ancestry of a group of organisms. • Importantly, it is a directed tree, starting from a unique node known as the recent common ancestor. • Basically, the roots of the phylogenetic tree describe this recent common ancestor. KKR1116 10
- 12. EXAMPLE OF ROOTED TREE KKR1116 12
- 13. UNROOTED TREE • The unrooted phylogenetic tree is a type of phylogenetic tree that only describes the relatedness of a group of organisms. • Importantly, the leaf nodes of this type of phylogenetic tree only show relatedness, not the ancestry. • Hence, it does not start with the recent common ancestor and does not contain a root. KKR1116 13
- 15. EXAMPLE OF UNROOTED TREE KKR1116 15
- 16. KKR1116 16
- 17. Construction of phylogenetic tree There are two different methods based on which phylogenetic tree is constructed. A. Distance based method B. Character based method i. Maximum parsimony . ii. Maximum likelihood. KKR1116 17
- 18. Distance Base Method This method is based on the amount of the distance or the dissimilarity between the two aligned, sequences. in this method of constructing the phylogenetic tree The sequence data is transformed into pairwise distance and then the matrix is used for building a tree KKR1116 18
- 19. Construction of phylogenetic tree by distance based method 1. ATCGTGGTACTG 2. CCGGAGAACTAG 3. AACGTGCTACTG 4. ATGGTGAAAGTG 5. CCGGAAAACTTG 6. TGGCCCTGTATC KKR1116 19
- 20. A. ATCGTGGTACTG B. CCGGAGAACTAG C. AACGTGCTACTG D. ATGGTGAAAGTG E. CCGGAAAACTTG F. TGGCCCTGTATC KKR1116 20
- 21. A B C D E F A 9 2 4 9 10 B 9 6 2 10 C 5 9 10 D 6 10 E 10 F A B C E KKR1116 21
- 22. A/C B D E F A/C 9 4.5 9 10 B 6 2 10 D 6 10 E 10 F A/C B/E D F A/C 9 4.5 10 B/E 6 10 D 10 F A C D E B KKR1116 22
- 23. FINAL STEP A/C/D B/E F A/C/D 7.5 10 B/E 10 F F E B D C A KKR1116 23
- 24. KKR1116 24
- 25. MAXIMUM PARSIMONY • It is a method to find out the tree which has small possible number of mutations. • It is a method which uses only few characters. KKR1116 25
- 26. Maximum parsimony taxon 1 2 3 A G G G B G T G C T G T D T T T G G T T A B C D KKR1116 26
- 27. Maximum likelihood • It is a method of construction of phylogenetic tree by the probability method. • By finding the probability between two characters or sequences the tree is constructed. KKR1116 27
- 28. KKR1116 28
- 29. Significanceof phylogenetictree It is the fundamental tool to derive their most useful evidence from the fields of anatomy, embryology, paleontology and molecular genetics. Used in search of new species. Used to study evolutionary histories. KKR1116 29
- 30. To study how species were spread geographically. To study common ancestors of extant and extinct species. To represent evolutionary relationships between organisms that are believed to have some common ancestry. With the help of phylogenetic tree, the infectious microbes can be traced along with their evolutionary histories. KKR1116 30
- 31. references • NCBI • Cold spring harbor protocol. • Phylogenetic tree -Full theory explanation CSIR – NET (YouTube) KKR1116 31
- 32. Thank you . KKR1116 32
Editor's Notes
- #22: is what the completed table looks like 03:12 with the table completed we can move to 03:15 the next step which is to use the table 03:17 to identify the sequences with the 03:19 fewest differences between them 03:20 we will infer that these are the 03:23 sequences that are the most closely 03:24 related to one another in our table we 03:28 see that the sequences with the fewest 03:30 differences between them are a and C 03:32 with only two differences as well as B 03:35 and E that also only have two 03:37 differences between them with this 03:40 information we can draw the first 03:42 groupings on our phylogenetic tree will 03:46 group a and C together to reflect the 03:48 fact that these two sequences show the 03:50 closest relationship we have here to one 03:52 another and we'll group B and E together 03:54 to reflect the fact that they also show 03:57 an equivalently close relationship to 03:59 one another with the first two groupings 04:02 made on a tree we now need to rework our 04:05 table with the grouped sequences 04:07 combined together as a grouping rather 04:09 than to individual entries in the table 04:11 we'll start by combining a and C this 04:14 group to do this will take the average 04:17 difference that a and C show to each of 04:21 the other sequences let's start with the 04:23 differences they show to be we see there 04:26 are nine differences between a and B and 04:28 nine differences between C and B 04:31 so the average difference of a and C to 04:33 be is nine and we can make that entry on 04:36 our new table let's move to the next 04:40 position D we can see there are four 04:44 differences between a and D and there 04:46 are five differences between C and D so 04:49 the average difference of a and C to D 04:52 is four point five and we can add that 04:54 entry on a new table we can complete the 04:58 rest of the table in this way we have an 05:01 average of nine differences between a 05:03 and C to e and ten differences to F the 05:07 rest of the table can be copied down 05:09 from the first table with the AC 05:13 grouping now added to our new table we 05:15 can proceed to also add the B e grouping 05:18 and to complete the table with B and E 05:21 grouped together using the same approach 05:23 as before for B and E we have an average 05:27 of nine differences to the AC group we 05:31 have four point five for a C to D and 05:33 ten for a C to F for B and E to D we 05:39 have an average of six differences and 05:42 an average of ten for being a to F and 05:45 there are also ten differences between 05:46 DNF with this table completed we can now 05:52 proceed to the next step this step is to 05:55 identify the sequences with the fewest 05:56 differences between them in our new 05:58 table we can see that the AC group has 06:02 only four point-five differences to D so 06:05 this is the next close relationship in 06:07 our tree and we can add this next 06:10 grouping to a tree like this with D as 06:13 the next grouping out from a and C 06:16 reflecting the fact that D is more 06:18 closely related to them than it is to 06:21 the other sequences we have with this 06:23 new grouping added to the tree we need 06:25 to rework our table again with the AC D 06:28 grouping incorporated we have an average 06:31 of 7.5 for AC and D to the B e group and 06:36 we have an average of 10 for AC and D to 06:39 F and we also have ten differences 06:41 between the B e group and half 06:44 with the new table completed we can now 06:48 determine the next relationship by 06:50 identifying the sequences in the table 06:51 with the fewest differences between them 06:53 again we can see that this is the ACD 06:56 group with the be e group with an 06:59 average of 7.5 differences so we can add 07:03 the next grouping to the tree like this 07:06 grouping the ACD group with the be e 07:09 group this now leaves us with one more 07:13 sequence F that is equally distantly 07:16 related to all the other sequences with 07:18 ten differences to each of them so we 07:21 can add this last grouping to the tree 07:22 like this reflecting the distant 07:25 relationship between F and all the other 07:28 sequences and this completes our 07:31 phylogenetic tree built from these six 07:34 DNA sequences the bet that we use to 07:38 build this tree is a distance method 07:40 specifically an approach called 07:42 unweighted pair group method with 07:44 arithmetic mean or upgma and th