ELE4120 Tutorial 8

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ELE4120 BioinformaticsTutorial 8

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Content

Classifying Organisms

Systematics and Speciation

Taxonomy and phylogenetics

Phenetics versus cladistics Phylogenetic trees

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Biological classification

Goal:

To develop a system of categories that

provides (useful) information aboutliving things

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Classifying Organisms Systematics is the science of the relationships

of organisms how organisms are related and the evidence for those

relationships

Speciation -- the origin of new species from

previously existing ones anagenesis - one species changes into another over time

cladogenesis - one species splits to make two

Reconstruct evolutionary history

Phylogeny

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In the western scientific tradition:

1. Biological Taxonomy - Aristotle - mid 300s BCE2. Hierarchical Taxonomy & Binomial

nomenclature - Linnaeus - early to mid 1700s

3. Phenetic taxonomy - Adanson - 1750s

4. Phylogeny - Darwin, Haeckel - mid 1800s

5. Evolutionary taxonomy - Mayr and Simpson -mid 1900s

6. Phenetic taxonomy - Sneath and Sokal - 1960s

7. Cladistic taxonomy - Hennig - 1960s

Biological classification History

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Species Classification Phenetic: physical attributes, numerical

taxonomy (resemblance: Based on phenotypic similarity)

Cladistic (Phylogenetic): evolutionaryrelationships (descent: Based exclusively on the branching

patterns of phylogeny )

Evolutionary: synthesis of the two

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Phenetic Classification Like with like

Use many characters to define overallsimilarity

Linnaean

God created, Linneaus arranged

Before Darwin so not based on Evolution (but

may reflect history) Problem: uses all types of characters

(analogies, ancestral & derived

homologies)

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Taxonomy and phylogenetics Taxonomy is the science of the classification of

organisms

Taxonomy deals with the naming and ordering of taxa.

The Linnaean hierarchy:

1. Kingdom2. Division

3. Class

4. Order

5. Family6. Genus

7. Species

Taxonomic Classification

of Man

Homo sapiens

Superkingdom: Eukaryota

Kingdom: Metazoa

Phylum: Chordata

Class: Mammalia

Order: Primata

Family: Hominidae

Genus:

Species:

Homo

sapiens

Subspecies: sapiens

Evolution

ary

distanc

e

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Classification Systems Taxonomy:

Classification of living organisms into groups

Phylogenetic Classification System:

Groups reflect genetic similarity andevolutionary relatedness

Phenetic Classification System:

Groups do not necessarily reflect geneticsimilarity or evolutionary relatedness. Instead,

groups are based on convenient, observable

characteristics.

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Phylogenetics

Phylogenetics is the science of the pattern of evolution

Evolutionary theory states that groups of similar

organisms are descended from a common ancestor.

Phylogenetic systematics is a method of taxonomic

classification based on their evolutionary history.

Evolutionary biology versus phylogenetics Evolutionary biology is the study of the processes

that generate diversity

Phylogenetics is the study of the pattern of diversityproduced by those processes

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Pheneticsversus cladistics Within the field of taxonomy there are two different

methods and philosophies of building phylogenetic trees:cladistic and phenetic

Phenetic methods construct trees (phenograms) byconsidering the current states of characters without regard to theevolutionary history that brought the species to their current

phenotypes;dendrograms are based on overall similarity

Cladistic methods construct trees (cladograms) rely onassumptions about ancestral relationships as well as on current

data;cladograms are based on character evolution (e.g. sharedderived characters)

Cladistics is becoming the method of choice; it is considered tobe more powerful and to provide more realistic estimates,however, it is slower than phenetic algorithms

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Phenetic Classification ofVertebrates

Fish Frogs Sala. Turtles Lizards Crocs. Birds Mammals

Amphibians Reptiles Birds Mammals

Are the

pheneticreptiles a

valid

phylogenetic

group?

To create aphylogenetically valid

class of reptiles, what

groups would need tobe included?

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Phenetic Classification of

Vertebrates

Fish Frogs Sala. Turtles Lizards Crocs. Birds Mammals

Amphibians Reptiles Birds Mammals

Are the

pheneticreptiles a

valid

phylogenetic

group?

Reptiles

To create aphylogenetically valid

class of reptiles, what

groups would need tobe included?

Possible Phylogenetic Classification of Vertebrates

MammalsAmphibians

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Character and Distance DataThe molecular data used to generate

phylogenetic trees fall into one of twocategories:

1. Characters: a well-defined feature that can

exist in a limited number of different states.

2. Distances: a measure of the overall,

pairwise difference between two data sets.

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Phylogenetic trees The central problem of phylogenetics:

--how do we determine the relationships between taxa?

in phylogenetic studies, the most convenient way of presenting evolutionary

relationships among a group of organisms is the phylogenetic tree

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Phylogenetic trees Node: a branchpoint in a tree (a presumed ancestral OTU)

Branch: defines the relationship between the taxa in terms of

descent and ancestry Topology: the branching patterns of the tree

Branch length (scaled trees only): represents the number ofchanges that have occurred in the branch

Root: the common ancestor of all taxa

Clade: a group of two or more taxa or DNA sequences that includesboth their common ancestor and all their descendents

Species A

Species E

Species D

Species C

Species BRoot

Branch

CladeNode

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Phylogenetic trees There are many ways of drawing a tree

A

E

D

C

B

A DCB

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=

A DCB E DC B A

=

E CD B A

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A DCBA DCB

= =

A DCB

no meaning

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A DCB A DCB

Bifurcation

Trifurcation

=/

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Phylogenetic trees Trees can be scaled or unscaled (with or without branch lengths)

A

E

D

C

B

A

E

D

C

B

A

D

C

B

A D

C

B

unit

unit

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Phylogenetic trees Trees can be unrooted or rooted

D

A C

B

Unrooted tree

A CB D

Root

Rooted tree

D

A C

B

Root

A CB D

Root

Root

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Phylogenetic trees Trees can be unrooted or rooted

Unrooted tree

A C

B D

4

3

5

2

1

These trees show five different evolutionary relationships among the taxa!

Rooted tree 1

B

A

C

D

Rooted tree 2

A

B

C

D

Rooted tree 3

A

B

C

D

Rooted tree 4

C

D

A

B

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Example : Cladograms--Restate steps in other words

1) select group of organisms

2) determine characters & states3) for each character, classify ancestral &derived

- comparison to outgroup- traits shared with outgroup = ancestral

4) group by shared derived characters(synapomorphies)

5) choose most parsimonious tree

(fewest evolutionary transitions)

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Example : Seed Plants

presentPresentPresent1Monocots

---2Outgroup

PresentPresent-2Gnetales

PresentPresentPresent2Dicots

Present--2Conifers

SeedsPerianthCarpelsCotyledon

#

TAXA

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Example : Parsimonious Tree

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ELE4120 Tutorial 8