1. Phylogenetics

2. Review Multiple sequence alignment ClustalW
Steps 1.  pairwise alignments 2.  UPGMA or Neighbor-Joining tree based on pairwise scores (guide tree) 3.  Multiple alignment informed by guide tree

3. Multiple sequence alignment (Phylip format)
ThNM012b TTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TGTGCCCCCG GGGCCCGTGC
ThNM TTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TGTGCCCCCG GGGCCCGTGC
ThNM TTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TGTGCCCCCG GGGCCCGTGC
ThlanugQH0 TTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TGTGCCCCCG GGGCCCGTGC
ThNM TTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TGTGCCCCCG GGGCCCGTGC
ThNM TTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TGTGCCCCCG GGGCCCGTGC
ThNM TTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TGTGCCCCCG GGGCCCGTGC
ThNM TTCCGCCGGG GGGGTNGTCC CNNGGCTCGG TGTGCCCCCG GGGCCCGTGC
ThNM TTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TGTGCCCCCG GGGCCCGTGC
ThNM CTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TTT--TGCCG GGGCGCGTGC
ThNM CTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TTT--TGCCG GGGCGCGTGC
Talthermo CTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TTT--TGCCG GGGCGCGTGC
ThNM CTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TTT--TGCCG GGGCCCGTGC
ThNM CTCCGCCGGG GGGGTCGTCC CGGGGCGCGG TTT--TGCCG GGGCCCGTGC
AfumHQ6310 GGCCGCCGGG GAGGC-CTTG CGC CCCC- GGGCCCGCGC
ThNM0026A -GCCGCCGGG GAGGC-CTTG CGC CCCC- GGGCCCGCGC
ThNM025a -GCCGCCGGG GAGGC-CTTG CGC CCCC- GGGCCCGCGC
Aspni GCCGCCGGG GGGGCGCCTC TGC CCCCC GGGCCCGTGC
ThNM CCGCCGGG GGGCGTGTCC CGC CCCC- GGGCCCGCGC
ThaurantT8 --CCGCCGGG GGGCGTGTCC CGC CCCC- GGGCCCGCGC

5. Newick tree format ( Physella_anatina/gb|AY651175.:0.00993,
Physa_heterostropha/gb|AY6511: ,
Physa_acuta/gb|AY |: )
: )
: ,
Physella_virgata/gb|AY : ,
Lymnaea_stagnalis/gb|EF : ,
Lymnaea_neotropica/emb|AM49400: )
: ,
Biomphalaria_glabrata/gi|34538: )
: );

10. Branch length may or may not reflect distance or time

11. A B C A B C A B C Three possible rooted trees with three taxa
(unrooted tree has no meaning with 3 taxa)

12. A B A C A D A B C D C D B D C B
Four possible unrooted trees with four taxa

13. Characters and character states
Important terms
Characters and character states
Ancestral versus derived
(not primitive versus advanced)

14. Invertebrate Fish Humans Dogs Birds animals
Some examples of ancestral and derived characters
Invertebrate
Fish
Humans
Dogs
Birds
animals
Upright
posture
loss of
body hair
feathers and
feathered wings
bony limbs
bony skeleton
nervous system
Note:
Ancestral and derived are relative terms. In this tree, a character
is ancestral to nodes higher in the tree, but derived with respect to nodes
Lower in the tree.

15. The problem of taxonomy not reflecting phylogeny

16. polyphyletic groups contain taxa that are not derived from a single common ancestor
Old groups “algae” and “fungi” were polyphyletic
Brown
Algae
Oomycete
Fungi
Green
Plants
Green
Algae
True
Fungi
animals

17. paraphyletic (subset of polyphyletic) groups have a taxonomic group contained within another group of equal status

18. Old “Reptilian” class is paraphyletic
Crocodiles
Birds
Lizards

19. Estimating phylogeny (phylogenetics)
Distance methods (not “phylogenetic”)
- Examples: UPGMA, Fitch-Margolish, Neighbor Joining
- Begin with a single measure of similarity or distance for every pair of taxa
Phylogenetic methods (“phylogenetic”)
- Examples: parsimony, maximum likelihood, Bayesian (Mr.Bayes)
- Look at multiple discrete characters and use differences among character states to infer phylogeny

20. Distance (also sometimes called numerical) methods rely on a single numerical value that expresses the difference or similarity for any given pairwise comparison. With DNA data this value is usually obtained by dividing number of matching nucleotide positions by the average length of the two sequences compared.
Species 1:   CTGATCCGAGGTCAACCTTGGGTT-GTGAAGGTCGTTTTACGGCTGGAAC                 |||||||||||||||||||||| | | ||||||||||||||||||||||| species 2:      562 CTGATCCGAGGTCAACCTTGGGGTCGCGAAGGTCGTTTTACGGCTGGAAC 513

22. Estimating phylogeny (phylogenetics)
Distance methods (not “phylogenetic”)
- Examples: UPGMA, Fitch-Margolish, Neighbor Joining
- Begin with a single measure of similarity or distance for every pair of taxa
Phylogenetic methods (“phylogenetic”)
- Examples: parsimony, maximum likelihood, Bayesian (Mr.Bayes)
- Look at multiple discrete characters and use differences among character states to infer phylogeny

24. Character #2 - + - + - - + + - + + -
A B C D A C B D A D B C
Tree # Tree # Tree #3

25. Some potential pitfalls with molecular data

26. Paralogs versus Orthologs
Orthologs - homologous genes that reflect speciation
Paralogs - homologous genes that reflect gene duplication = members of a gene family in a single organism (examples: alpha versus beta hemoglobin; red versus green visual pigment proteins
Important to distinguish between these when doing comparative analyses (It’s sometimes hard to tell)

27. The Problem of Multiple Hits

29. Among other problems, this causes “long-branch attraction”

30. Scoring in phylogenetic methods is model dependent

31. General idea applies to protein amino-acid sequences as well

32. Can convert to scoring matrix based on
log probablilities

33.
Physa_hete AA CATTATATTT
Physa_acut AC CATTATATTT
Physella_a AA CATTATATTT
Physella_v AA CATTATATTT
Lymnaea_st TTTAT
Lymnaea_ne GATATTGGTA CTTTATATAT
Biomphalar TTGCGTTGAC TCTTTTCAAC AAACCATAAA GATATTGGTA CTTTGTACAT
AATTTTTGGG ATCTGGTGTG GATTGGTCGG TACAGGTTTA AGCTTGTTAA
AATTTTTGGT GTTTGATGCG GTTTAGTGGG AACAGGTTTA TCCTTATTAA
AATCTTTGGA ATCTGATGCG GGTTAGTAGG GACTGGATTG TCTTTATTAA
AATTTTTGGA ATTTGGTGTG GTCTAGTTGG TACTGGATTA TCATTATTGA
etc.

34. Bootstrap Analysis

35.
Physa_hete AA CATTATATTT
Physa_acut AC CATTATATTT
Physella_a AA CATTATATTT
Physella_v AA CATTATATTT
Lymnaea_st TTTAT
Lymnaea_ne GATATTGGTA CTTTATATAT
Biomphalar TTGCGTTGAC TCTTTTCAAC AAACCATAAA GATATTGGTA CTTTGTACAT
AATTTTTGGG ATCTGGTGTG GATTGGTCGG TACAGGTTTA AGCTTGTTAA
AATTTTTGGT GTTTGATGCG GTTTAGTGGG AACAGGTTTA TCCTTATTAA
AATCTTTGGA ATCTGATGCG GGTTAGTAGG GACTGGATTG TCTTTATTAA
AATTTTTGGA ATTTGGTGTG GTCTAGTTGG TACTGGATTA TCATTATTGA
etc.