Topic 3: Systematics II
Schools of Systematics
What are the schools of thought of systematics?
How does one make a cladogram?
What are higher taxa & ranks?
•
• If the system is based on evolution, then it is
phylogenetic
How should they be used in this course?
• These underlying principles are typically
evolution and parsimony
Applying phylogenies – Evolution and
homoplasy in Anolis
Schools of Systematics
Systematics – The clustering of groups or
organisms based on a unifying set of principles
(evolutionary, or otherwise)
Evolutionary
Systematics
Phenetics
Cladistics
Model-based
approaches
______________
______________
______________
______________
What is Evolutionary Systematics?
Oldest approach to reconstructing phylogeny
__________________
Often ______ objective – “Anything goes”
What is Evolutionary Systematics?
An evolutionary tree
Note: ancestors, time, and anagenesis
Ancestors occur and time is recognized
Anagenesis is recognized
Both monophyletic and ______________ groups
are recognized
No longer used
Basal Archosaur
Time
What is Evolutionary Systematics?
Clustering is based on both _____________ and
________________ features
Evolutionary trees are produced
No explicit procedure to reconstructing phylogeny
The scientist’s opinions about character weighting
and relationships are important
Basal Diapsid
Basal Sauropsid
Basal Amniote
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What is Phenetics?
A response to the lack of objectivity of
Evolutionary Systematics
Not necessarily __________________
What is Phenetics?
By looking at gross similarity, the analysis can be
confounded by _______________ and
__________________
Modern uses:
‘True’ evolutionary relationships are not knowable
Measures overall ______________ among taxa
Low taxonomic levels
Morphometrics and some immunological data
Does not differentiate between ancestral and derived
(characters are not polarized)
Explicit quantitative procedure
What is Cladistics?
Also called Phylogenetic Systematics
What is Phenetics?
A ______________________ is produced
Note confounding effects of anagenesis and
convergence
Evolutionary Tree
Originated in the 1950s by Hennig,
popularized in the 1960s, further developed
after that
Response to the need for a ______________
system that was ________________ and
_________________
Therefore, phylogenetic
Phenogram
What is Cladistics?
Also called Phylogenetic Systematics
Only ____________________ are used
to cluster taxa hierarchically
__________________, not anagenesis,
is the focus of cladistics
Premise that little is known about
character evolution
What is Cladistics?
Also called Phylogenetic Systematics
Used extensively from the 1960s to
present day
Used to reconstruct phylogeny and
study character evolution
Well implemented in computer
algorithms
Not explicitly model-based
Parsimony is the guiding principle
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Cladistics: How to make a cladogram
_______________
Timeless and without
ancestors
A representation of
character state
distribution
An hypothesis of
relationship
_______ an
evolutionary tree
(OG (A (B (C, D))))
Cladistics: How to make a cladogram
A
B
C
D
E
How do these “Caminacules” differ from
one another?
Cladistics: How to make a cladogram
A
B
C
D
E
Code each of the characters (columns) in a table (taxa in rows)
1. Single or close together hind limbs (0), OR 2 separate hind limbs (1)
2. Front limbs are short (0), OR lengthened (1)
3. Abdomen is unpatterned (0), OR patterned (1)
4. Abdomen is flat (0), OR bulbous (1)
5. Two (0) front limbs, OR four (1)
6. One or no eyes (0), OR two laterally-directed eyes (1)
1
Cladistics: How to make a cladogram
Taxon
A
1
2
3
4
5
6
B
C
D
E
Cladistics: How to make a cladogram
A
B
C
D
E
1
What is the likelihood approach?
Cladistics: How to make a cladogram
However, with many taxa, finding
the best topology is
computationally intensive
With m taxa, then number of rooted
topologies, n, is:
n=
(2m − 3)!
m− 2
2 (m − 2)!
Developed in the 1960s to present
Places phylogenetic reconstruction in an
explicitly ____________________ framework
Realization that we do know things about
character evolution, particularly DNA
Find the tree with the greatest likelihood:
If m = 5, then n = 7!/(8 x 6) = 105
L ∝ P( Data | Tree)
Maximum parsimony __________
___________________________
___________________________
What is Bayesian Inference?
Developed in 1764 by Thomas Bayes
Applied to phylogenetics in 1996
Builds on likelihood approaches by also allowing
for the incorporation of ___________________
Allows calculation of the actual probability of a
tree:
L
P( data | tree) P(tree)
P (tree | data ) =
P(data )
Why are model-based approaches so powerful?
Both likelihood and Bayesian approaches are
computationally intensive
Allow us to use knowledge of character evolution in
reconstructing phylogeny, which parsimony doesn’t
really do
Primarily applied to DNA sequence data, but
recently, even morphological data can by used
Why are model-based approaches so powerful?
What do we know about DNA evolution?
(More in other classes)
1
What are higher taxa and ranks?
What are higher taxa and ranks?
What do they mean?
Domain
Kingdom
Phylum
Class
Order
Family
Genus
• Erected to recognize diversity in Archae,
Eubacteria, Eukarya
• Major divisions within Eukarya (Plantae,
Animalia, Fungi, etc.)
• Distinct body plans within Animalia (Plantae
and Fungi use Divisions)
Domain
Kingdom
Phylum
Class
Order
Family
Genus
• Some sub-groupings
Species
Species
Subspecies
Subspecies
• ____________________________________
• Some distinct group within a species?
Ranks
What do they mean?
Are they real?
Are they comparable?
How should they be used?
Hierarchical framework of
classification
What are higher taxa and ranks?
• 3 domains are monophyletic, no evidence
that a Domain is something biologically real
• Most are monophyletic, no evidence of
biological reality
• Recent evidence suggests that evolution of
developmental genetic “kernels” defined
__________ before the Cambrian explosion*
Domain
Kingdom
Phylum
Class
Order
• _________________ of biological reality
Family
Genus
Species
Subspecies
• Most scientists agree that species are actual
___________________________
• Little evidence for biological reality
* Davidson & Erwin. 2006. Science 311:796.
What are higher taxa and ranks?
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Subspecies
What are higher taxa and ranks?
Are they real?
How should they be used?
Most don’t have a specific meaning,
are not biological entities, and aren’t
comparable to other groups of the
same rank
Trend to not use ranks
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Subspecies
Are they comparable?
Families of Urodela (Salamanders):
Fig. 3-1: Pough et al. 2004.
An Example – Evolution & Homoplasy in Anolis
• Approximately 400 species of Anolis, ~125 of which
occur in the Caribbean
Including this course!
Use monophyletic groups (clades) to
refer to higher taxa
_________________ are obviously
useful, maybe _____________ as well
Photos © AS Munoz, G White, J Hance, PJ Bergmann
1
An Example – Evolution & Homoplasy in Anolis
Anolis Ecomorphs
• Many species occur in the Caribbean
• On the Greater Antilles, “___________” have evolved
Twig giant
• The same ______________, with similar morphology
and ecology, have evolved on each of the four big
islands
Crown giant
© J. Losos
Trunk-crown
Trunk-crown dwarf
© Auburn Herp Soc
Cuba
Haiti/Dominican Rep.
Trunk-ground
Jamaica
Puerto
Rico
Powell and Russell, 1992.
Homoplasy in Anolis – different phylogenetic signal
from different datasets
© Reptilien-Center.de
Replicate Evolution in Anolis
Locomotor
Morphology
mtDNA
Sequences
Anolis ecomorphs evolved in a ______________
______________ on each of the Greater Antilles
From Jackman et al., 2000.
From Jackman et al., 2000.
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