ELE4120 Tutorial 8
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Transcript of 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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Phylogenetic trees There are many ways of drawing a tree
=
A DCB E DC B A
=
E CD B A
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Phylogenetic trees There are many ways of drawing a tree
A DCBA DCB
= =
A DCB
no meaning
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Phylogenetic trees There are many ways of drawing a tree
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