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Phylogeny and the
Tree of Life

Contents
1
2
3
4
5

Investigating the Tree of Life
Phylogenies Show Evolutionary Relationships
Binomial Nomenclature
Linking Classification and Phylogeny
What We Can and Cannot Learn From Phylogenetic
Trees
6 Shared Characters Are Used to Construct
Phylogenetic Tree
7 Gene Duplication and Gene Families
8 Molecular Clock

Phylogeny and the Tree of Life
I
...


Phylogenies Show Evolutionary Relationships
- organisms share homologous characteristics because of common ancestry

III
...


Felidae

2=represents the most
common ancestor of
coyotes and gray wolves

Taxidea taxus

Lutra
1= represents the most
recent common ancestor
of all the members of the
weasels (Mustelidae) and
dog (Canidae) families

Panthera pardus

Taxidea
Carnivora

Panthera

Lutra lutra

Mustelidae

1
Canis latrans
Canidae

Canis

2
Canis lupus

-

-

-

Phylocode: recent approach in aligning Linnaen classification with phylogeny in
which only names groups that include a common ancestor and all of its
descendants
phylogenetic tree represents a hypothesis about evolutionary relationships
o these relationships are often depicted as a series of dichotomies, or two
way branch points
o each branch point represents divergence of two evolutionary lineages from
a common ancestor
sister taxa: groups of organisms that share an immediate common ancestor and
hence are each other’s closest relatives
rooted: means that a branch point within the tree represents the last common
ancestor of all taxa in the tree
polytomy: a branch point from which more than two descendant groups emerge
o indicates the evolutionary relationships among the descendants taxa are
not yet clear

Branch Point (Node)

Taxon A
2
Taxon B
Sister
Taxa

4
Taxon C

ANCESTRAL
LINEAGE

1
Taxon D

This branch point
represents the most recent
common ancestors of taxa
A-F

3

Taxon E

Taxon F

This branch point form a
polytomy: an unresolved
pattern of divergence

V
...


Shared Characters are Used to Construct Phylogenetic Tree
- cladistics: approach to systematics where common ancestry is the primary
criterion used to classify organisms
o clades: groups of species, each of which includes an ancestral species and
all of its descendants
o clades, like taxonomic ranks, are nested within larger clades
 monophyletic: consists of an ancestral species and all its
descendants
 paraphyletic: consists of an ancestral species and some, but not all
of its descendants
 polyphyletic: includes taxa with different ancestors

MONOPHYLETIC
GROUP

POLYPHYLETIC
GROUP

PARAPHYLETIC
GROUP
A

A

B

B

C

C

D

D

E

E

F

F

G

G

A

B

C

D

E

F

VII
...


Gene Duplication
and Divergence

Species A

Molecular Clock
- a yardstick for measuring the absolute time of evolutionary change based on the
observation that some genes and other regions of genomes appear to evolve at
constant rates
- the assumption underlying is that the number of nucleotide substitutions in
orthologous genes is proportional to the tine that has elapsed since the species
branched from their common ancestor (divergence time)
- in case of paralogous genes, the number of substitutions is proportional to the
time since the genes became duplicated



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