C.DARWIN ( )

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1 C.DARWIN ( )

2 LAMARCK Each evolutionary lineage has evolved, transforming itself, from a ancestor appeared by spontaneous generation DARWIN All organisms are historically interconnected. Their relationships may be represented with a genealogical (phylogenetic) tree.

4 PHYLOGENY The history of descent of a group of taxa, such as species, from their common ancestor(s), including the sequence of ramifications and, sometimes, divergence times; it applies also to the genealogy of genes derived from an ancestral common gene IT IS REPRESENTED WITH A PHYLOGENETIC TREE

5 "The affnities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species... The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classifcation of all extinct and living species in groups subordinate to groups... From the frst growth of the tree, many a limb and branch has decayed and dropped off, and these lost branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only from having been found in a fossil state... As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all a feebler branch, so by generation I believe it has been with the Tree of Life, which flls with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifcations" (Charles Darwin, 1859) (Charles Darwin, 1859)

6 Constructing phylogenetic trees implies reviving the Darwinian idea that a species originates from another species, and that similar species have common ancestors.

7 .and the same idea is extended backward through time.

8 .down to the origin of life on Earth TREE OF LIFE

9 PHYLOGENETIC TREE

10 TREES, NOT LADDERS! Aristotele

11 a phylogenetic tree is built using characters APOMORPHY: The derived (new) state of a character PLESIOMORPHY: The ancestral (ancient) state of a character SYNAPOMORPHY A derived character state (apomorphy) which is shared by two or more taxa, and is supposed to have beed inherited from the same common ancestor

12 SYNAPOMORPHY: A shared derived character state

13 SYNAPOMORPHY: A shared derived character state

14 A character must be HOMOLOGOUS, in order to be considered a synapomorphy similar anatomy Same embryonic origin

15 CONSTRUCTING A PHYLOGENETIC TREE

16 nested hierarchy

18 The "dichotomic" nature of phylogenetic trees lies on the fact that the origin of diversification of living organisms (what determines their phylogeny) is a process of differentiation of two evolutionary lineages which depart from their common ancestor (CLADOGENESIS)

19 TWO ASPECTS OF DARWINIAN EVOLUTION ANAGENESIS: Directional evolution (of a character) WITHIN a single evolutionary lineage CLADOGENESIS: The ramification of a phylogenetic tree through speciation events

20 SPECIATION Speciation Speciation is is aa diversification diversification event event along along an an evolutionary evolutionary lineage lineage which which produces produces two two or or more more different different species species

21 SPECIATION Speciation is the core of evolution Without speciation there would be no diversification, nor adaptive radiations, therefore the evolutionary process would be much more limited

22 SPECIATION SPECIATION is is the the evolution evolution of of mechanisms mechanisms of of reproductive reproductive isolation, isolation, i.e. i.e. Barriers Barriers to to gene gene flow flow among among populations populations

23 Sometimes, it is difficult to reconstruct the sequence of the events of diversification which have occurred in large numbers in a short period of evolutionary time ciclidi

24 A polytomy underlies the failure of resolving the phylogeny of a given group of taxa

25 A phylogenetic tree may - or may not have a root rooted tree unrooted tree

26 rooting an "unrooted" tree

27 The The Newick Newick format format

28 We can calculate the number of trees (topologies) which exist given the number of taxa (OTUs) rooted trees unrooted trees where n is the number of taxa

29 The number of possible trees increses with the increase of the number of taxa

30 Note that the # of unrooted trees with n OTUs is equal to the # of rooted trees with n-1 OTUs

31 A phylogenetic tree may also contain information relative to the quantity of evolution occurred along each single branch ccladogram ladogram phylogram phylogram

32 CONSTRUCTING A PHYLOGENETIC TREE Choose taxa Choose the characters Identify the characters possessed by each taxon Construct the tree that minimizes the numbers of evolutionary changes (PARSIMONY)

33 an example of matrix for the vertebrate tree

35 The principle of PARSIMONY 6 steps 7 steps

36 CONSTRUCTING A PHYLOGENETIC TREE USING DNA (OR PROTEIN) SEQUENCES Choose taxa Select genes Sequence the genes Align the sequences Construct the tree on the basis of the selected reconstruction method

37 DNA is the genetic material

38 Genetic information is encoded in long uninterrupted sequences of DNA. In such sequences, single GENES are recognizable; they encode for proteins through the translational system of a DNA sequence into an amino acid sequence.

39 THE GENETIC CODE

40 A protein is synthesizes as an amino acid chain on the basis of the nucleotide sequence of the gene by which the protein is encoded

41 Biological information always has the form of a sequence

42 ALIGNMENT

45 an alignment of sequences is nothing else a matrix of characters (taxon x character).. which can be analyzed with a similar approach

47 Maximum Parsimony tree 20 steps

48 Maximum Parsimony tree 20 steps

49 MAXIMUM PARSIMONY Is a method based on discrete characters Is a method based on an optimization criterion

50 MAXIMUM PARSIMONY

51 TYPES OF CHARACTERS Discrete characters taxon x character Genetic distances taxon x taxon

52 GENETIC DISTANCES THey can be easily calculated as the percentage of different nucleotides (or amino acids) in a sequence Nucleotide substitutions: 99/468 = 21.15% Amino acid substitutions: 1/156 = 0.64%

53 MATRIX OF GENETIC DISTANCES (taxon x taxon)

54 UPGMA Unweighted Pair-Group Method with Arithmetic Means

56 MULTIPLE SUBSTITUTIONS

57 The existence of multiple substitutions suggests that estimates of genetic distance based on the simple counting of nucleotide differences may well represent an underestimation of the "real" distance The size of the underestimation will become higher as phylogenetic distance increases (i.e.: as long as the time of divergence increases)

59 Jukes-Cantor (1969) (one-parameter model)

60 Kimura (1980) (two-parameter model)

63 TYPES OF METHODS OF RECONSTRUCTION Based on an algorithm Based on an optimization criterion

64 METHODS BASED ON AN OPTIMIZATION CRITERION A matrix is established An optimization criterion is chosen All possible topologies are drawn The best tree is chosen on the basis of the selected criterion

65 MAXIMUM LIKELIHOOD incorporates information on a model of evolution(jc, K2P, GTR, )

66 BOOTSTRAP

POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics

POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics - in deriving a phylogeny our goal is simply to reconstruct the historical relationships between a group of taxa. - before we review the