Download • Evolutionary relationships are documented by creating a branching

Molecular Phylogenetics
Phylogenetics
•In the lectures on molecular evolution we shifted our
focus onto longer evolutionary times. Instead of
thinking about time passing in generations, we want to
consider millions of years instead.
• Evolutionary theory states that groups of similar
organisms are descended from a common ancestor.
•We can use phylogenetic trees to visualise and analyse
evolution over very long periods.
• Phylogenetic systematics (cladistics) is a method of
taxonomic classification based on their evolutionary
history.
•If we had complete, reliable information, we could draw
the relationship of species as a branching tree, where
each branching event represents a speciation event.
• It was developed by Willi Hennig, a
German entomologist, in 1950.
Cladistic Methods
• Evolutionary relationships are documented by
creating a branching structure, termed a
phylogeny or tree, that illustrates the
relationships between the sequences.
• Cladistic methods construct a tree
(cladogram) by considering the various
possible pathways of evolution and choose
from among these the best possible tree.
• A phylogram is a tree with branches that are
proportional to evolutionary distances.
time
1
NODE
Hypothetical
Taxonomic Unit
C
A
BRANCH
D
B
ROOT
Operational
Taxonomic
Unit (OTU)
A
C
B
D
E
E
time
UNROOTED
ROOTED
There are two kinds of information contained within a phylogenetic tree:
1. Branching order (topology) indicates the relative closeness of
different taxa
Trees may be rooted (we know which taxa are older or younger),
or unrooted
2. Branch lengths indicate the amount of divergence
Cladogram
Phylogram
os
o
Monophyletic, paraphyletic, and polyphyletic groupings
a
ph
Hair
Grouping 2
se
Grouping 1
ou
an
at
R
d
Grouping 3
M
Leopard
um
Bir
Turtle
H
t
sh
ele
Fi
nc
Am
La
ibia
n
Dr
il
ph
D
E
G
H
J
K
D
E
G
H
J
K
D
E
G
H
J
K
Salamander
Amniotic egg
C
F
I
C
F
I
C
F
I
Tuna
Lamprey
Four walking legs
Hinged jaws
Lancelet (outgroup)
Vertebral column
B
B
A
(a) Monophyletic. In this tree, grouping 1,
consisting of the seven species B– H, is a
monophyletic group, or clade. A monophyletic group is made up of an
ancestral species (species B in this case)
and all of its descendant species. Only
monophyletic groups qualify as
legitimate taxa derived from cladistics.
B
A
(b) Paraphyletic. Grouping 2 does not
meet the cladistic criterion: It is
paraphyletic, which means that it
consists of an ancestor (A in this case)
and some, but not all, of that ancestor’s
descendants. (Grouping 2 includes the
descendants I, J, and K, but excludes
B–H, which also descended from A.)
A
(c) Polyphyletic. Grouping 3 also fails the
cladistic test. It is polyphyletic, which
means that it lacks the common ancestor
of (A) the species in the group. Furthermore, a valid taxon that includes the
extant species G, H, J, and K would
necessarily also contain D and E, which
are also descended from A.
2
Birds
Molecular Evolution
Crocodiles
Snakes and
lizards
Turtles and
tortoises
REPTILES
Mammals
The reptiles group, which excludes birds, is a paraphyletic
group. Reptiles + birds together form a monophyletic
group.
DNA is a good tool for taxonomy
DNA sequences have many advantages over
classical types of taxonomic characters:
– Character states can be scored unambiguously
– Large numbers of characters can be scored for
each individual
– Information on both the extent and the nature of
divergence between sequences is available
(nucleotide substitutions, insertion/deletions, or
genome rearrangements)
• Phylogenetics often makes use of numerical data,
(numerical taxonomy) which can be scores for various
“character states” such as the size of a visible
structure or it can be DNA sequences.
• Similarities and differences between organisms can
be coded as a set of characters, each with two or
more alternative character states.
• In an alignment of DNA sequences, each position is a
separate character, with four possible character
states, the four nucleotides.
We rarely, if ever, know the species relationship, so
we infer the phylogeny from biological data –
morphological or molecular (DNA, protein
sequence)
We can study evolutionary relationships by analysing
DNA sequence divergence. Aims:
1. Discover order of sequence/species divergence
2. Discover time of divergences
3. Describe sequence of events in lineage
3
DNA sequences start evolving independently after
speciation events. Sequences accumulate differences
over time.
most closely related organisms should be the most
similar at the molecular level.
Convergent evolution is
a problem
Convergent evolution of analogous burrowing
characteristics
Australian marsupial
mole
Homology vs. Analogy
Human arm vs bat wing
• Homology: similar by descent; likeness in structure is due
to trait inherited from common ancestor. Example: human
hand and bat wing
• Analogy: correspondence in function between anatomical
parts of different structure and origin. Examples: Marsupial
mole vs N. American mole
Porcupine quill and cactus spine.
Divergence of species from a
common ancestor
Leopard
Domestic cat
Domestic cats did
not evolve from leopards
N. American mole (placental mammal)
Common ancestor
4
•In terms of DNA comparison, the simplest measure of level of
similarity is obtained by counting the number of nucleotide
differences. This is much less ambiguous than methods using
morphological characters. We can develop statistical models for the
accumulation of differences.
•The molecular clock can be used to estimate the relative time of
divergence of several species based on the level of DNA sequence
similarity in a given homologous gene. This information can be used to
construct phylogenetic trees.
•We prefer Molecular data over Morpholgical data because:
1.DNA is strictly heritable, whereas morphological characteristics will
be affected by the environment (non-heritable differences)
2.DNA can be described unambiguously (sequence of base pairs)
whereas there are often classification differences of morphological
characters
3.We have clear models of how DNA and proteins evolve over time,
but the models for morphological evolution are unclear
4.DNA /protein is more amenable to mathematical analysis
5.It is very easy to assess homology (relationship by descent) of
DNA/protein sequences
6.Possible to perform very distant comparisons of DNA/protein
•The DNA sequences are
compared and the levels of
similarity or dissimilarity are
used to arrange the species’
relationships into the
phylogenetic tree shown on
the left.
•The DNA sequences are
aligned (lined up with each
column corresponding to the
same base-pair in the
ancestor). This is often called
a multiple alignment, and
columns are often called
sites in the alignment.
7.DNA is abundant (found in all life)
5