Transcript Document 7508590

Phylogeny:
Reconstructing Evolutionary Trees
(Part 2)
Chapter 14
1
Cladistic vs. phenetic trees
• Cladistic trees are built from shared derived
characters (synapomorphies), which are assumed
to be homologous unless there is good reason
(deeper analysis, parsimony) to believe otherwise
– requires polarizing characters or character states
– only synapomorphies are “informative”
– methodology is explicitly phylogenetic
• Phenetic trees are based on overall similarity
– Phenetic trees are phylogenetic only to the extent that
degree of similarity = closeness of relationship
2
An example to show how cladistic and phenetic
approaches can result in different trees – 1
• Four taxa (W, X, Y, Z) and five characters (1 – 5),
each of which has two “states”
Characters
Taxon
1
2
3
4
5
W
a*
b*
c
d
e
X
a*
b*
c*
d*
e*
Y
a*
b
c
d
e
Z
a
b
c
d
e
3
An example to show how cladistic and phenetic
approaches can result in different trees – 2
• Matrix of shared character states (similarity matrix):
Number of similar character states
Taxon
W
X
Y
Z
W
–
X
2
Y
4
Z
3
–
1
–
0
4
–
• Start tree by pairing taxa W and Y, then assess similarities
between W/Y, X, and Z (could also have started with Y/Z pair)
4
An example to show how cladistic and phenetic
approaches can result in different trees – 3
• Three “taxa” (W/Y, X, Z) and four characters (1 – 5), each
of which has two “states” (discard character 2 because W
and Y do not share the same state)
Characters
Taxon
1
2
3
4
5
W/Y
a*
–
c
d
e
X
a*
–
c*
d*
e*
Z
a
–
c
d
e
5
An example to show how cladistic and phenetic
approaches can result in different trees – 4
• Start tree by pairing taxa W and Y, then assess similarities between
W/Y, X, and Z
Number of similar character states
Taxon
W/Y
X
Z
W/Y
–
1
3
–
0
–
X
Z
In step 2, we pair W/Y with Z, and we are finished
6
Phenogram 1 for taxa W, X, Y, and Z
Y
Z
X
Decresasing similarity
W
7
Phenogram 2 for taxa W, X, Y, and Z
Z
Y
X
Decresasing similarity
W
8
Phenogram 3 for taxa W, X, Y, and Z
Y
Z
X
Decresasing similarity
W
9
Phenogram – summary
• Our phenetic analysis strongly indicates that W, Y,
and Z form a similar group that is quite different
from X
• If we use this as an estimate of phylogeny, we
conclude that W, Y, and Z are more closely related
to one another than either is to X
• This is essentially the Unweighted Pair-Group
Method (UPGMA)
10
A cladistic analysis of the same data
• The character states are now polarized
(perhaps by comparison to an outgroup),
such that the character states with asterisks
(*) represent the derived character states
11
The character state matrix
• Four taxa (W, X, Y, Z) and five characters (1 – 5), each of
which has two “states” (* = derived state)
Characters
Taxon
1
2
3
4
5
W
a*
b*
c
d
e
X
a*
b*
c*
d*
e*
Y
a*
b
c
d
e
Z
a
b
c
d
e
12
The character state matrix
• Four taxa (W, X, Y, Z) and five characters (1 – 5), each of
which has two “states” (* = derived state)
Characters
Taxon
1
2
3
4
5
W
a*
b*
c
d
e
X
a*
b*
c*
d*
e*
Y
a*
b
c
d
e
Z
a
b
c
d
e
13
The character state matrix
• Four taxa (W, X, Y, Z) and five characters (1 – 5), each of
which has two “states” (* = derived state)
Characters
Taxon
1
2
3
4
5
W
a*
b*
c
d
e
X
a*
b*
c*
d*
e*
Y
a*
b
c
d
e
Z
a
b
c
d
e
14
Cladogram for taxa W, X, Y, and Z
W
X
Y
Z
c*,d*,e*
b*
a*
a,b,c,d,e
15
Phenogram 3 for taxa W, X, Y, and Z
Y
Z
X
Decresasing similarity
W
16
Cladogram – summary
•
•
•
•
There is only one most parsimonious cladogram
Only characters 1 and 2 are informative (synapomorphies)
W and X are sister taxa
Z is the most distantly related of the four taxa, rather than
closely related to W and Y
• The reason that X appears unrelated to the other three taxa
in the phenogram is because X has three autapomorphies
that make it dissimilar to the other three taxa.
17
Phylogeny and Classification – 1
• Linnaean classification is based historically on
morphological traits — it is a phenetic classification system
• Species are defined by type specimens
– similar species are grouped into a genus
– genera, families, orders, classes, phyla, kingdoms
• Linnaeus lived a century before Darwin – he was not an
evolutionist and did not believe that his classification
system described evolutionary relationship
• Darwin, however, recognized that the ability to construct a
hierarchical classification system based on similarity is
exactly what would be expected under his concept of
evolutionary history as a tree that described descent from
nested sets of common ancestors
18
Phylogeny and Classification – 2
• Should classification reflect phylogeny?
• If our phylogeny of the whales and artiodactyls is
correct, then whales are just a subgroup of the
Order Artiodactyla, not an order of their own
(Cetacea)
• Recognizing Cetacea as a separate order on a par
with artiodactyls makes Artiodactyla a
paraphyletic taxon – a taxon that does not include
all the descendants of its common ancestor
19
Phylogeny of whales and artiodactyls based on
presence/absence of SINEs and LINEs (Nikaido et al. 1999)
(Fig. 14.8)
Red line encloses
traditional artiodactyl
species
20
A monophyletic group: all the decendants of a common
ancestor (+ the common ancestor) (Fig. 14.10a)
21
A paraphyletic group: does not include all the descendants of
the common ancestor (Fig. 14.10b)
22
Examples of paraphyletic taxa (Fig. 14.10c)
23
A polyphyletic group: does not include the common ancestor
(Fig. 14.10b)
1
2
3
4
5
24
How to classify?
• A strict cladistic classification scheme would require a
taxonomic level for every level of branching in a
phylogeny – might be extremely unwieldy
• Just about everyone would probably agree that polyphyletic
taxa should be avoided (suggests non-existent evolutionary
relationship)
• Evolutionary classification:
– Recognizes “grade” as well as clade as a basis for classification
– Cetacea are sufficiently different (adaptations for fully aquatic
existence) from other mammals that they should be given the status
of an order, equivalent to the other orders of mammals (Primates,
Carnivora, Rodentia, Artiodactyla, etc.)
– Paraphyletic taxa are justified when a great deal of
morphological/physiological change occurs along one branch of a
clade
25
Reptilia as a paraphyletic taxon
• Virtually all cladistic analyses of birds and reptiles
agree that crocodilia and birds are sister groups –
that is, crocodiles are more closely related to birds
than to other conventional reptiles such as snakes
and lizards
• Putting birds in the class Aves makes the class
Reptilia paraphyletic
• The justification is that birds (warmblooded,
feathers, flight) seem to have attained a different
grade than reptiles (cold blooded, no feathers)
26
Phylogeny of the main vertebrate groups:
reptiles are a paraphyletic group, made up of turtles, lizards,
snakes, and crocodiles
Fish
Amphib.
Turtles
Mammals
Lizards
Snakes Crocs
Birds
27
Phylogeny of the main vertebrate groups:
reptiles are a paraphyletic group, made up of turtles, lizards,
snakes, and crocodiles
Fish
Amphib.
Turtles
Mammals
Lizards
Snakes Crocs
Birds
28
Bootstrapping Trees – 1
• How much confidence do we have in any
particular tree?
• How dependent is it on the particular set of
characters that we have analyzed?
• Would we have obtained the same tree if we had
analyzed a different set of characters?
• To answer these questions, we use the statistical
technique known as bootstrapping
29
Bootstrapping Trees – 2
• Suppose the actual data sample consists of n observations
• To bootstrap, draw a new “sample” of n observations from
the actual data, with replacement, and re-analyze the
bootstrap sample
• Repeat many times (1,000’s) the process of drawing a
bootstrap sample and analyzing it
• For a phenogram or cladogram, the “data” that are
bootstrapped are the characters – in other words, we resample the characters that we analyze to make the tree
• Tests with known phylogenies (lab experiments) indicate
that bootstrap support of 70% or better is usually associated
with the true phylogeny.
30
Co-speciation of aphids and bacterial symbionts (Fig. 14.14)
31
Using phylogenies to test evolutionary
hypotheses
• Co-speciation: do parasites speciate when
their hosts speciate (“vertical speciation”),
or do parasites speciate by lateral transfer to
a new host (“horizontal speciation”)?
• What is the order of evolution of
adaptations?
• Does continental drift explain the pattern of
speciation in a taxon?
32
• Families that
include eusocial
species are
indicated in
boldface type
Sociality and
nesting
behavior in
hymenoptera
(Hunt 1999)
(Fig. 11.13
33
Phylogeography of Chameleons (Fig. 14.13)
•
•
•
•
Separation of Gondwanaland
Upper graph is phylogeny of chameleons
based on sequence of separation of southern
continents (vicariance hypothesis)
Lower graph is phylogeny estimated from
morphological, behavioral, and molecular data
(Raxworthy et al. 2002). This tree implies that
chameleons have dispersed from Madagascar
to Africa on several occasions, from
Madagascar to the Seychelles, and from Africa
to India
The dispersal hypothesis is supported by the
presence of chameleons on Reunion and the
Comoros Is., which are volcanic and have
never been in contact with continental land
masses.
34
Phylogeography
of Chameleons
(Fig.
14.13c)
35
Are
ungulates
monophyletic?
(Fig.
14.16)
•
According to
this figure, are
the ungulates
(artiodactyls and
perissodactyls) a
monophyletic
group?
36
Are
ungulates
monophyletic?
(Fig.
14.16)
•
•
•
According to
this figure, the
ungulates
(artiodactyls and
perissodactyls)
are a
paraphyletic
group
Hooves gained
Hooves lost
37
Are
ungulates
monophyletic?
(Fig.
14.16)
•
•
According to
this figure, the
ungulates
(artiodactyls and
perissodactyls)
are a
polyphyletic
group
Hooves gained
38
Are these trees different? (Fig. 14.17)
39