phylogeny_cladistics
DESCRIPTION
University BiologyTRANSCRIPT
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Phylogeny & Cladistics
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Objectives
The basics of phylogenetic trees
How phylogenetic trees are constructed.
How phylogenies can address questions
about evolution.
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Our classifications
will come to be, as
far as they can be
so made, genealogies.
- Charles Darwin, 1859
Phylogeny and Classification
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Systematics is the study of biological diversity in an evolutionary context. It includes
speciation
taxonomy
**phylogeny
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How to classify life
Phenetic classification
Based on overall similarity
Those organisms most similar are classified
more closely together.
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Taxonomy is the branch of systematics concerned
with naming and classification.
Scientific names are binomials
Example: Acer saccharum
- Acer is the genus name - it is a Latin noun
- saccharum is the specific epithet - it is a Latin
adjective
Carolus Linnaeus
1707-1778
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Biological
classifications are
hierarchical: each
taxonomic group is
nested within a
more inclusive
higher order group.
(Note that only the genus name
and specific epithet are italicized.)
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Phylogeny and classification
Hierarchy
All taxonomic classifications are hierarchical how does phylogeny differ?
Class
Order
Family Family
Genus
Species 1
Species 2
Species 3
Species 4
Species 1
Species 2
Species 3
Genus
Genus
Species 1
Species 2
Order
Family
Genus
Species 1
Species 2
Species 3
Species 4
Species 5
Species 6
Species 7
Species 8
Species 9
Genus
Species 1
Species 2
Species 1
Genus
Species 1
Species 2
Species 3
Genus
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Problem with phenetic classification:
Can be arbitrary, e.g., classify these:
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Phylogenetic classification
Based on known (inferred) evolutionary
history.
Advantage:
Classification reflects pattern of evolution
Classification not ambiguous
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Phylogeny is the study of the
pattern of divergence history.
(as opposed to speciation, which
addresses process.)
Assembling a phylogeny
using cladistics, taxa are
associated on the
basis of shared evolutionary
innovations.
Willi Hennig, 1913 - 1976
Founder of Phylogenetic
Systematics
(also called cladistics)
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Hierarchy
Phylogenetic (cladistic) classification reflects evolutionary history
The only objective form of classification organisms share a true evolutionary history regardless of our arbitrary decisions of how to classify them
Phylogeny and classification
Class
Order
Order
Family
Family
Family
Genus
Genus
Genus
Genus
Genus
Genus
FamilyGenus
Genus
PhylogenyClassification
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Phylogeny
Phylogenetics: the study of ancestor descendent relationships. The objective of phylogeneticists is to construct phylogenies
Phylogeny: A hypothesis of ancestor descendent relationships.
Phylogenetic tree: a graphical summary of a phylogeny
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Phylogeny
ALL life forms are related by common ancestry anddescent. The construction of phylogenies provides
explanations of the diversity seen in the natural world.
Phylogenies can be based on morphological data,
physiological data, molecular data or all three.
Today, phylogenies are usually constructed using
DNA sequence data
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Phylogenetic Characters
We use characters to construct phylogenies. A characteris any attribute of an organism that can provide us withinsights into history (shared ancestry).
In molecular phylogenies, characters are typicallynucleotide positions in homologous gene sequence, andeach position can possess four CHARACTERSTATES: A,C, G, or T
Cladograms are constructed based on the similarities ofhomogolous DNA sequences
Mutations in the ancestral gene results in all descendantpossessing the new (derived) trait
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A B C D E F
TIME
speciation
Cladogram or Phylogenetic Tree
TAXA
Phylogenetic Trees
The point at which branching occurs (node) signifies a speciation event from a common ancestral population
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Fig. 26-5
Sister taxa (B & C more related to each other than to A)
ANCESTRAL LINEAGE
Taxon A
Polytomy (ancestral group
splits into more
than two Taxa
Common ancestor of
taxa AF
Branch point
(node)
Taxon B
Taxon C
Taxon D
Taxon E
Taxon F
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Apomorphy (derived trait)
= a new, derived feature
E.g., for this evolutionary transformation
scales --------> feathers
(ancestral feature) (derived feature)
Presence of feathers is an apomorphy
for birds.
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Taxa are grouped by apomorphies
Apomorphies are the result of evolution.
Taxa sharing apomorphies
underwent same evolutionary history
should be grouped together.
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Phylogeny and classification
Classification
Note that taxa are nested
on the basis of shared
common ancestors
e.g., All tetrapods share
a common ancestor with
legs, but other chordates
outside of Tetrapoda do
not share this common
ancestor
The traits mapped onto
the phylogeny are
synapomorphies we will return to them later
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Phylogeny and classification
Monophyletic group
Includes an ancestor
all of its descendants
A B C D
Paraphyletic group
Includes ancestor and
some, but not all of its
descendants
A B C D
Polyphyletic group
Includes two convergent
descendants but not their
common ancestor
A B C D
Taxon A is highly derived
and looks very different
from B, C, and ancestor
How could this happen? Taxon A and C share
similar traits through
convergent evolution
Only monophyletic groups (aka clades) are recognized in cladistic
classification
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Phylogeny and classification
Monophyly
Each of the colored lineages
in this echinoderm phylogeny
is a good monophyletic group (clade)
Asteroidea
Ophiuroidea
Echinoidea
Holothuroidea
Crinoidea
Each group shares a common
ancestor that is not shared by any
members of another group
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Lindblad-Toh et al. (2005) Nature 438: 803-819
Paraphyletic groups
Paraphyly
Foxes are paraphyletic with respect to dogs, wolves, jackals, coyotes, etc.
This is a trivial example because
fox and dog are not formal taxonomic units, but it does show
that a dog or a wolf is just a derived
fox in the phylogenetic sense
Foxes
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Lindblad-Toh et al. (2005) Nature 438: 803-819
Paraphyletic groups
Monophyly
Note that canids are still a good
monophyletic clade within Mammalia
Each of the colored lineages within
canids is also a monophyletic clade
Canids
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Paraphyletic groups
Fry et al. (2006) Nature 439: 584-588
Paraphyly
Lizards (Sauria) areparaphyletic with respect
to snakes (Serpentes)
Serpentes is a monophyletic
clade within lizards
Squamata (lizards + snakes)
is a monophyletic clade
sister to sphenodontida
Snakes are just derived,
limbless lizards
Lizards
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Paraphyletic groups
Paraphyly
Birds are more closely related
to crocodilians than to other
extant vertebrates
Archosauria = Birds + Crocs
We think of reptiles as turtles,
lizards, snakes, and crocodiles
But Reptilia is a paraphyletic
group unless it includes Aves
Reptilia
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What does this mean?
It means that
reptiles dontexist!
No, it means
that youre oneof us!
What it means is that reptile is only a valid clade if it includes birds
Birds are still birds, but Aves cannot be
considered a Class equivalent toClass Reptilia because it is evolutionarily
nested within Reptilia
Reptilia
Aves
(birds)
Turtles
Crocodiles
Lizards and snakes
Tuataras
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Review:
Introduction
to
Phylogenetic
Trees
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Cladisitc Character State Definitions
Plesiomorphy: refers to the ancestral character state
Apomorphy: a character state different than the ancestral state, also called a DERIVED STATE
Derived does not mean better or advanced (as the mutations that create them can be deleterious, neutral or beneficial)
Synapomorphy: a derived character state (apomorphy) that is SHARED by two or more taxa due to inheritance from a common ancestor: these character states are phylogenetically informative using the parsimony or cladistic criterion
Autapomorphy: a uniquely derived character state
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Constructing Phylogenetic Trees
We use homologous characters (synapomorphies) to construct phylogenetic trees and to identify groups that are monophyletic; synapomorphies are phylogenetically informative.
We want to avoid using homoplasious characters to construct phylogenies
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Character States
After Page and Holmes 1998
we will return
to this
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More Synapomorphies
sharedshared
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Homology and Homoplasy
A character state that is shared between two DNA sequences or taxa may be so because they inherited it from a common ancestor, or it is HOMOLOGOUS (a homology/ synapomorphy)
Alternatively, the shared character might occur because they were evolved independently, in which case they are called a HOMOPLASY
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Why can Homoplasy Occur?
After Page and Holmes1998
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Homoplasy and Polyphyly
Homoplasy results in erroneous, polyphyletic groupings
such as vultures
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A Vulture
Vultures are a polyphyletic group. New world and old world
vultures provide an example of homoplasy resulting from convergent
evolution.
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Analogy (non homology): The fins of a whale and
the fins of a shark are another example of homoplasy
due to convergence, the independent acquisition of a
character in different lineages
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Reversals & Phylogeny
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Parsimony (also known as cladistics)
The Principle of Parsimony: simple explanations
are preferred over more complicated ones.
In terms of phylogenetic trees, less evolutionary
steps are better than more steps to explain
relationships. The tree with the least number of
steps is the most parsimonious.
The parsimony method minimizes the total number of
evolutionary changes required to explain relationships
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Constructing Trees with Parsimony
Outgroup: When constructing a phylogeny for a group of organisms, we need to employ an outgroup, which is not part of the group of interest (the ingroup), but also not too distantly related to it.
The outgroup is used to polarize the character states, or infer change. The character state possessed by the outgroup is defined a priori as ancestral (pleisiomorphic)
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Whale Evolution
Ambulocetus
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The Artiodactyla
The artiodactyla are a group of hoofed mammals
that possess an even number of toes, and includes
camels, pigs, peccaries, deer, the hippopotamus,
cattle and giraffes. The perissodactyla are hoofed
mammals that possess an odd number of toes (e.g.
horses, rhinos, tapirs).
Are whales really a member of the artiodactyla?
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Selecting Phylogenetic Trees with
Parsimony
Figure 4.8, pg. 121
Whales early Whales late
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Parsimony
using
morphologyFigure 14.5, pg. 558
Outgroup is a Perissodactyl
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Parsimony
using
molecular
characters
Figure 14.6, pg. 559
Site 142 is plesiomorphic (uninformative)
Site 192 is a autapomorphic (uninformative)
Sites 162, 166 & 177 are synapomorphies (informative)
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What do the informative sites tell us
about whale phylogeny?
Site 162 & 166 conflict with site 177
Hence there is homoplasy in the data set.
What is the most parsimonious tree looking at all characters?
Whales early 47 nt changes
Whales late 41 nt changes
Whales late has less evolutionary steps to explain relationships: the
most parsimonious explanation