Evolutionary relationships and finding new drugs in daffodils

Evolutionary relationships and finding new drugs in daffodils 1) Constructing phylogenies (working out evolutionary relationships) a) Why constructing phylogenies (or understanding evolutionary relationships) is important. b) How phylogenies are constructed. 2) Using phylogenies to help in the search for new drugs a) Creating a useful phylogeny. b) Choosing species to investigate.

Why constructing phylogenies (or understanding evolutionary relationships) is important. Look at these 3 articles and use your own thoughts to explain why scientists may be interested in understanding evolutionary relationships.

Why constructing phylogenies (or understanding evolutionary relationships) is important

How phylogenies are constructed

An example of a phlogenetic tree Gorillas Humans Chimpanzees

How many possible trees for 3 species?

How many possible trees for 3 species? C A B B A C A B C So there are 3 possible trees for 3 species

How many possible trees for 4 species?

How many possible trees for 4 species? D D D C C C B B B A A A C B A D C B A A C B B C C B D D C D D So there are 12 of one shape and 3 of another making 15 possible trees overall for 4 species A A A D C B B B C C D D

Choosing the most likely evolutionary tree 1. Identifying evolutionary change in Amino acids

1. Galanthus nivalis (Common snowdrop) 2. Narcissus cernuus 3. Narcissus tazetta 4. Narcissus asturiensis 1 a. 2 a. 3 a. 4 a. INRNLLLSTM VNRNLLLSTM NNKVSFFSKD NNRVSFFSKD IYRIDDNVRN RVRYFSTYFR GVRDFSTYFR GVRYFSTYFR NKYTCTYPHE NKYTYTHPHE NKYTYTYPHE NKYTYTHPHE SDNTMLFPLL VLGLFTLFIG VLVLFPLFIG VLVLFTLFIG 1 b. 2 b. 3 b. 4 b. SKDSSDWYEF AKDSSDWCEF LKNVVFSVSI LKNAVFSVSI ALFGLFVASI LYGSVYSSLQ FYGSVYSSLQ LYGSVYSSLQ NLGLVNSFVK KSPKRILLDQ KNPKRILLDQ VK AQ VK VQ AIGIHFDRGV AIGIHFDLGV AIGIHFDRGV IDFDLLSKWI IDFDLLSKWL TPYADFFHPN TPSADFFHPN TPPADFFHPN

Choosing the most likely evolutionary tree 2. Mapping characters onto possible evolutionary trees

93 S→P Narcissus cernuus Narcissus asturiensis Narcissus tazetta All orange characters (positions 1, 31, 45, 63 and 114) occur once each on all trees on the Narcissus branch just after G. nivalis branches off. 93 S→P C 93 Y→S Narcissus tazetta Narcissus cernuus Narcissus asturiensis 93 S→P 93 Y→S Galanthus nivalis A Galanthus nivalis Narcissus tazetta Narcissus asturiensis Narcissus cernuus Galanthus nivalis All blue characters (positions 13, 47, 101, 108 and 162) occur once each on tree C but have to occur twice each on trees A and B. B 93 Y→S All yellow characters occur once each on all trees. Positions 34, 66, 68 and 161 at the tip where N. cernuus is. Position 131 at the tip where N. tazetta is. Position 152 at the tip where N. asturiensis is.

Identifying the informative characteristics

Identifying the informative characteristics Number in the key Description of amino acid variation Informative characteristic? 1 (Green) All amino acids the same No 2 (Orange) Amino acid only common to all 3 Narcissus species No 3 (Yellow) Amino acid different in only one Narcissus species No 4 (Blue) 2 species have one amino acid and the other 2 have a different one Yes 5 (White) Position 93 No The informative ones are shared, derived characteristics

Creating a useful phylogeny

Amino acid at each position number Species 13 34 47 75 78 93 101 108 112 131 142 152 162 Galanthus nivalis (Common snowdrop) = outgroup K Y Y H R Y S Y K L L S K Narcissus asturiensis R Y H H R P A C K L L N Q Narcissus atlanticus K Y Y R R S S C K L F S K Narcissus calcicola K Y Y H R S S C K L F S K Narcissus cernuus R D H H L S A C K L L S Q Narcissus jacetanus R Y H H R P A C K L L N Q Narcissus longispathus K Y Y H R S A C Q L L S Q Narcissus nevadensis K Y Y H R S A C Q L L S Q Narcissus pseudonarcissus R Y H H R S A C K L L N Q Narcissus scaberulus K Y Y R R S S C K L F S K Narcissus serotinus K Y Y H R S S Y K F L S K Narcissus tazetta K Y Y H R S S Y K F L S K Narcissus triandrus R D H H L S A C K L L S Q

Amino acid at each position number Species 13 34 47 75 78 93 101 108 112 131 142 152 162 Galanthus nivalis (Common snowdrop) = outgroup K Y Y H R Y S Y K L L S K Narcissus asturiensis R Y H H R P A C K L L N Q Narcissus atlanticus K Y Y R R S S C K L F S K Narcissus calcicola K Y Y H R S S C K L F S K Narcissus cernuus R D H H L S A C K L L S Q Narcissus jacetanus R Y H H R P A C K L L N Q Narcissus longispathus K Y Y H R S A C Q L L S Q Narcissus nevadensis K Y Y H R S A C Q L L S Q Narcissus pseudonarcissus R Y H H R S A C K L L N Q Narcissus scaberulus K Y Y R R S S C K L F S K Narcissus serotinus K Y Y H R S S Y K F L S K Narcissus tazetta K Y Y H R S S Y K F L S K Narcissus triandrus R D H H L S A C K L L S Q

Amino acid at each position number Species 13 34 47 75 78 93 101 108 112 131 142 152 162 Galanthus nivalis (Common snowdrop) = outgroup K Y Y H R Y S Y K L L S K Narcissus serotinus K Y Y H R S S Y K F L S K Narcissus tazetta K Y Y H R S S Y K F L S K Narcissus calcicola K Y Y H R S S C K L F S K Narcissus atlanticus K Y Y R R S S C K L F S K Narcissus scaberulus K Y Y R R S S C K L F S K Narcissus longispathus K Y Y H R S A C Q L L S Q Narcissus nevadensis K Y Y H R S A C Q L L S Q Narcissus cernuus R D H H L S A C K L L S Q Narcissus triandrus R D H H L S A C K L L S Q Narcissus pseudonarcissus R Y H H R S A C K L L N Q Narcissus jacetanus R Y H H R P A C K L L N Q Narcissus asturiensis R Y H H R P A C K L L N Q There are many equally correct ways of organising the table but for the next step to work all of the green blocks in any column need to be next to each other.

Amino acid at each position number Species 13 34 47 75 78 93 101 108 112 131 142 152 162 Galanthus nivalis (Common snowdrop) = outgroup K Y Y H R Y S Y K L L S K Narcissus serotinus K Y Y H R S S Y K F L S K Narcissus tazetta K Y Y H R S S Y K F L S K Narcissus calcicola K Y Y H R S S C K L F S K Narcissus atlanticus K Y Y R R S S C K L F S K Narcissus scaberulus K Y Y R R S S C K L F S K Narcissus longispathus K Y Y H R S A C Q L L S Q Narcissus nevadensis K Y Y H R S A C Q L L S Q Narcissus cernuus R D H H L S A C K L L S Q Narcissus triandrus R D H H L S A C K L L S Q Narcissus pseudonarcissus R Y H H R S A C K L L N Q Narcissus jacetanus R Y H H R P A C K L L N Q Narcissus asturiensis R Y H H R P A C K L L N Q This is quite a complicated tree. Remember that evolutionary relationships don’t alter if nodes are rotated so the same tree can actually look very different if several of the nodes are rotated.

131 L→F 93 Y→S 75 H→R 112 K→Q 108 Y→C 101 S→A 162 K→Q 34 Y→D 78 R→L 142 L→F 13 K→R 47 Y→H N. jacetanus N. asturiensis N. pseudonarcissus N. triandrus N. cernuus N. longispathus N. nevadensis N. scaberulus N. atlanticus N. calcicola N. tazetta N. serotus G. nivalis Sheet 5 93 S→P 152 S→N

Choosing species to investigate

Narcissus tazetta Narcissus triandrus Narcissus pseudonarcissus Narcissus jacetanus

Choosing species to investigate i) Which species is most closely related to the species that has the lowest known IC 50 value? Maybe this one will have an even lower IC 50 value. Narcissus jacetanus has the lowest IC 50 value. From your evolutionary tree or from the on sheet 5 you should be able to see that Narcissus asturiensis is most closely related to N. jacetanus.

Choosing species to investigate ii) Which species is most closely related to the species that has the highest known IC 50 value? This is probably the species least likely to possess a useful new drug. Narcissus triandrus has the highest IC 50 value. From your evolutionary tree or from the on sheet 5 you should be able to see that Narcissus cernuus is most closely related to N. triandrus.

Choosing species to investigate iii) Are there any groups of species on the evolutionary tree that haven’t been studied at all? Maybe there are very different chemicals in some of these groups that might have a much lower IC 50 value than any that have been discovered before. Select 3 species that you think would be best to study first if we are aiming to make sure that we have investigated all groups of species. There are 3 groups of closely related species that haven’t been studied (see next slide) and you should have chosen one from each of them.

131 L→F 93 Y→S 75 H→R 112 K→Q 34 Y→D 78 R→L N. jacetanus N. asturiensis N. pseudonarcissus N. triandrus N. cernuus N. longispathus N. nevadensis N. scaberulus N. atlanticus N. calcicola N. tazetta N. serotus G. nivalis Sheet 5 93 S→P 152 S→N 142 L→F 13 K→R 47 Y→H 101 S→A 162 K→Q 108 Y→C You should have selected one species from each of the blue blocks

Choosing species to investigate iv) Use your evolutionary tree to identify the species most closely related to the one from the research article. Maybe this species also has chemicals that will help in the fight against bird flu. Narcissus tazetta is the species from the research article. From your evolutionary tree or from the on sheet 5 you should be able to see that Narcissus serotus is most closely related to N. tazetta.

Summary You should have: • Identified reasons why understanding evolutionary relationships is important. • Investigated numbers of possible trees. • Used amino acid sequences to work out the most likely evolutionary tree for 3 species of Narcissus. • Identified which types of characteristic are useful for determining the most likely evolutionary tree. • Identified these characteristics in amino acid sequences of 12 different species of Narcissus. • Used this information to construct the most likely evolutionary tree for these 12 species. • Used your evolutionary tree and information from research articles to suggest which species to investigate for new drugs.