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Evolutionary Analysis. Tree Mathematical structure Model evolutionary history.

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Presentation on theme: "Evolutionary Analysis. Tree Mathematical structure Model evolutionary history."— Presentation transcript:

1 Evolutionary Analysis

2 Tree Mathematical structure Model evolutionary history

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4 Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6

5 Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 Sister taxa Outgroup Root Branch Node Tip Polytomy (more than one branch emerging from one node)

6 (a) The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. Camel Peccary Pig Hippo Whale Deer Cow Astragalus (ankle bone) ARTIODACTYLS Gain of pulley- shaped astragalus

7 (b) If whales are related to hippos, then two changes occurred in the astragalus. Camel Peccary Pig Hippo Whale Deer Cow ARTIODACTYLS Gain of pulley- shaped astragalus Loss of pulley- shaped astragalus

8 (a) The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. (b) If whales are related to hippos, then two changes occurred in the astragalus. Camel Peccary Pig Hippo Whale Deer Cow Camel Peccary Pig Hippo Whale Deer Cow (c) Data on the presence and absence of SINE genes support the close relationship between whales and hippos. Cow Locus Deer Whale Hippo Pig Peccary Camel Astragalus (ankle bone) 1  gene present 0  gene absent ?  still undetermined Whales and hippos share four unique SINE genes (4, 5, 6, and 7) ARTIODACTYLS Gain of pulley- shaped astragalus Loss of pulley- shaped astragalus Gain of pulley- shaped astragalus

9 Phylogenetic Tree shows ancestor-descendent relationships among populations or species clarifies evolutionary relationships

10 Root Ancestor of all sequences on tree

11 Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 Sister taxa Outgroup Root Branch Node Tip Polytomy (more than one branch emerging from one node)

12 Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 Taxon 1 Taxon 3 Taxon 2 Taxon 4 Taxon 5 Taxon 6

13 (a)(b) (c)

14 (a)(b) (c) =

15 Types of Trees Rooted Unrooted

16 Rooted Trees Node identified as root, from which all other nodes descend Have direction corresponding to evolutionary time

17 Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 Sister taxa Outgroup Root Branch Node Tip Polytomy (more than one branch emerging from one node)

18 Unrooted Trees Lacks root Does not specify evolutionary relationships Nothing about ancestors and descendents

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20 Unrooted Trees Lacks root Does not specify evolutionary relationships Nothing about ancestors and descendents Many tree-building programs generate unrooted trees!

21 Types of Trees Cladogram Phylogram

22 Cladogram

23 Relative recency of common ancestry

24 Cladogram

25 Relative recency of common ancestry Does not show amount of evolutionary change

26 Phylogram

27 Also contains branch lengths Numbers associated with branches Amount of evolutionary change

28 Phylogram

29 Cladogram Phylogram

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31 Constructing a Tree Construct multiple sequence alignment Build Tree Evaluate Tree

32 So how do I build a tree?

33 ylip/software.html#methods

34 So how do I build a tree?

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36 Tree building programs

37 Tree drawing programs

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39 FASTA alignment

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42 Newick Format (((((((Prochlorococcus_marinus: ,Synechococcus_BL107: ) : ,Cyanobium_PCC7001: ) : , Thiomicrospira_crunogena: ) : , Allochromatium_vinosum: ) : ,(Bradyrhizobium_BTAi1: , Nitrobacter_hamburgensis: ) : ) : , Halothiobacillus_neapolitanus: ) : , Acidimicrobium_ferrooxidans: ,Acidithiobacillus_ferrooxidans: );

43 Tree drawing programs

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48 File formats to save your tree

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51 Evaluating Trees Do your results make sense?

52 Evaluating Trees Do your results make sense? resample your data

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55 Bootstrap tree branch support values

56 Evaluating Trees Do your results make sense? resample your data ground-truth your data

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59 Organism Trees vs Gene Trees Don’t always match!

60 Homologs Orthologs separated by speciation Paralogs produced by gene duplication Xenologs result of horizontal gene transfer

61 Tree-building resources ylip/software.html#methods


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