c.darwin - unisi.itfalaschi/teaching/phylogenetictrees.pdf · plesiomorphy: the ancestral (ancient)...

C.DARWIN(1809-1882)

LAMARCK DARWIN

Each evolutionary lineage has evolved, transforming itself, from a ancestor appeared by spontaneous generation

All organisms are historically interconnected. Their relationships may be represented with a genealogical (phylogenetic) tree.

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

"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)

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

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

….down to the origin of life on Earth

TREE OF LIFE

PHYLOGENETIC TREE

TREES, NOT LADDERS!

Aristotele

APOMORPHY:The derived (new) state of a character

PLESIOMORPHY:The ancestral (ancient) state of a character

SYNAPOMORPHYA derived character state (apomorphy) which is shared by two or more taxa, and is supposed to

have beed inherited from the same common ancestor

a phylogenetic tree is built using characters

SYNAPOMORPHY:

A shared derived character state

SYNAPOMORPHY:

A shared derived character state

A character must be HOMOLOGOUS, in order to be considered a synapomorphy

similar anatomy

Same embryonic origin

CONSTRUCTING A PHYLOGENETIC TREE

nested hierarchy

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)

ANAGENESIS:Directional evolution (of a character) WITHIN a single evolutionary lineage

CLADOGENESIS:The ramification of a phylogenetic tree through speciation events

TWO ASPECTS OF DARWINIAN EVOLUTION

SPECIATION

Speciation is a diversification event along an evolutionary lineage which produces two or more different species

Speciation is a diversification event along an evolutionary lineage which produces two or more different species

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

SPECIATION is the evolution of mechanisms of reproductive isolation, i.e. Barriers to gene

flow among populations

SPECIATION is the evolution of mechanisms of reproductive isolation, i.e. Barriers to gene

flow among populations

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

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

A phylogenetic tree may - or may not - have a root

rooted tree unrooted tree

“rooting” an "unrooted" tree

The “Newick” format

The “Newick” format

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

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

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

A phylogenetic tree may also contain information relative to the quantity of

evolution occurred along each single branch

cladogramcladogram phylogramphylogram

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)

an example of matrix for the vertebrate tree

The principle of PARSIMONY

6 “steps” 7 “steps”

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

DNA is the genetic material

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.

THE GENETIC CODE

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

Biological information always has the form of a sequence

ALIGNMENT

an alignment of sequences is nothing else a matrix of characters (taxon x character)……..

……which can be analyzed with a similar approach

“Maximum Parsimony” tree

20 steps

20 steps

“Maximum Parsimony” tree

MAXIMUM PARSIMONY

• Is a method based on discrete characters

• Is a method based on an optimization criterion

MAXIMUM PARSIMONY

TYPES OF CHARACTERS

Discrete characters

Genetic distances

taxon x character

taxon x taxon

GENETIC DISTANCESTHey 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%

MATRIX OF GENETIC DISTANCES(taxon x taxon)

UPGMAUnweighted Pair-Group Method with Arithmetic Means

MULTIPLE SUBSTITUTIONS

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)

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

Kimura (1980)(two-parameter model)

TYPES OF METHODS OF RECONSTRUCTION

•Based on an algorithm

•Based on an optimization criterion

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

MAXIMUM LIKELIHOOD

incorporates information on a model of evolution(JC,

K2P, GTR, …)

BOOTSTRAP