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Phylogeny:Reconstructing Evolutionary Trees

(Part 2)Chapter 14

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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

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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

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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 – 2 4 3

X – 1 0

Y – 4

Z –

• 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)

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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

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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

X – 0

Z –

In step 2, we pair W/Y with Z, and we are finished

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Phenogram 1 for taxa W, X, Y, and Z

W Y XZ

Decresasing sim

ilarity

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Phenogram 2 for taxa W, X, Y, and Z

W Y XZ

Decresasing sim

ilarity

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Phenogram 3 for taxa W, X, Y, and Z

W Y XZ

Decresasing sim

ilarity

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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)

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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

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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

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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

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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

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Cladogram for taxa W, X, Y, and Z

W Y ZX

a,b,c,d,e

a*

b*

c*,d*,e*

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Phenogram 3 for taxa W, X, Y, and Z

W Y XZ

Decresasing sim

ilarity

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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.

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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

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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

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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

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A monophyletic group: all the decendants of a common ancestor (+ the common ancestor) (Fig. 14.10a)

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A paraphyletic group: does not include all the descendants of the common ancestor (Fig. 14.10b)

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Examples of paraphyletic taxa (Fig. 14.10c)

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A polyphyletic group: does not include the common ancestor (Fig. 14.10b)

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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

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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)

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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

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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

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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

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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 re-sample 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.

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Co-speciation of aphids and bacterial symbionts (Fig. 14.14)

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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?

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Sociality and nesting

behavior in hymenoptera (Hunt 1999) (Fig. 11.13

• Families that include eusocial species are indicated in boldface type

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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.

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Phylo-geography of Chame-

leons(Fig.

14.13c)

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Are ungulates

mono-phyletic?

(Fig. 14.16)

• According to this figure, are the ungulates (artiodactyls and perissodactyls) a monophyletic group?

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Are ungulates

mono-phyletic?

(Fig. 14.16)

• According to this figure, the ungulates (artiodactyls and perissodactyls) are a paraphyletic group

• Hooves gained

• Hooves lost

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Are ungulates

mono-phyletic?

(Fig. 14.16)

• According to this figure, the ungulates (artiodactyls and perissodactyls) are a polyphyletic group

• Hooves gained

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Are these trees different? (Fig. 14.17)