1. Chapter 26- Phylogeny and Systematics

2. Phylogeny is the evolutionary history of a species or group of related species
The discipline of systematics classifies organisms and determines their evolutionary relationships
Systematists use fossil, physical morphologies, and genetic data to infer evolutionary relationships
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3. Phylogeny and Systematics
History of a species, from origins to current time
Molecular systematics- DNA/RNA comparisons

4. Phylogenies “Origins of the tribe”
How they are determined:
Fossil record
Morphological homologies
Molecular homologies

5. Phylogenies “Origins of the tribe”
Fossil record- Relative dating can be used to come up with a loose timeline

6. 2. Morphological homologies
Living organisms having homologous structures or physical features that help determine a common ancestor. (IE- the forelimbs of mammals)
*Built the same, but different functions!

7. Phylogenies
**Do NOT get confused with analogous structures! (structures that are similar from CONVERGENT evolution, NOT from a common ancestor; same function, different built!

8. Example: Bat wings (bats are MAMMALS) A homologous structure would be the human forearm and an analogous structure would be a bird wing.

9. 3. Molecular homologies - DNA sequencing is one of the most powerful tools we can use to determine ancestors, even when an organism is extinct.

10. Molecular Homologies

11. Taxonomy Taxonomy is the ordered division and naming of organisms
In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances
Binomial Nomenclature - Genus and species.
2 naming system for every living organism = 2 Categories of Genus and species.
(IE. Panthera pardus or Homo sapiens)
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14. REMEMBER!
There are only 3 domains (Archaea, Bacteria, Eukarya) then then the pneumonic: “Dear King Phillip Came Over For Green Spaghetti”

15. Taxonomy of your Sticker Animal!

16. Q.Q. 4/10/19 Which of the following taxonomic names includes the fewest number of species? *use notes!
Animalia
Panthera
Felidae
Carnivora
Mammalia
Answer: b
This question focuses on Concept 26.1 (“Hierarchical Classification”). 16

17. Phylogenic Trees
Systematists depict hypotheses in evolutionary relationships in branching phylogenetic trees. Animation
Each branch point represents the divergence of two species
Sister taxa are groups that share an immediate common ancestor
A polytomy is a branch from which more than two groups emerge 

18. where lineages diverge Taxon A
Figure 26.5
Branch point:
where lineages diverge
Taxon A
Taxon B
Sister
taxa
Taxon C
Taxon D
Taxon E
ANCESTRAL
LINEAGE
Taxon F
Figure 26.5 How to read a phylogenetic tree.
Taxon G
This branch point
represents the
common ancestor of
taxa A–G.

19. Order Family Genus Species Panthera pardus (leopard) Felidae Panthera
Name the sister taxa!
Panthera
pardus
(leopard)
Felidae
Panthera
Taxidea
taxus
(American
badger)
Taxidea
Carnivora
Mustelidae
Lutra lutra
(European
otter)
Lutra
Figure 26.4 The connection between classification and phylogeny.
Canis
latrans
(coyote)
Figure 26.4 The connection between classification and phylogeny.
Canidae
Canis
Canis
lupus
(gray wolf)

20. Cladograms
In comparison with its ancestor, an organism has both shared and different characteristics.
A ancestral (primitive) character is a character that originated in an ancestor of the taxon
A shared derived character is an evolutionary novelty unique to a particular clade
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21. Sequence of events is NOT shown.
Shared characteristics shown in a cladogram (cladistics- the study of…).
Sequence of events is NOT shown.
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22. The outgroup is a group that has diverged before the ingroup
An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied
The outgroup is a group that has diverged before the ingroup
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23. Maximum Parsimony
Maximum parsimony - the simplest explanation with the fewest evolutionary events (appearances of shared derived characters)
Systematists can never be sure the best tree in a large data set and can narrow possibilities by applying the principles of maximum parsimony to determine the most likely option.
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24. (a) Percentage differences between sequences
Figure 26.14
Human
Mushroom
Tulip
Human
30%
40%
Mushroom
40%
Tulip
(a) Percentage differences between sequences
Figure Trees with different likelihoods.
Tree 1: More likely
Tree 2: Less likely
(b) Comparison of possible trees

25. **Nerd out with BLAST tutorial and BLAST sequencing! site
BLAST (basic local alignment search tool) is a computer program used to search for trees that are parsimonious and likely
**Nerd out with BLAST tutorial and BLAST sequencing! site
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26. Species  Species  Species           TECHNIQUE
Figure 26.15a
TECHNIQUE
Species 
Species 
Species  1
Figure Research Method: Applying parsimony to a problem in molecular systematics
Three phylogenetic hypotheses:  
 
 
  

27. TECHNIQUE Site 1 2 3 4 Species  C T A T Species  C T T C
Figure 26.15b
TECHNIQUE
Site 2 1 2 3 4
Species  C T A T
Species  C T T C
Species  A G A C
Figure Research Method: Applying parsimony to a problem in molecular systematics
Ancestral sequence A G T T

28. 3 4 TECHNIQUE RESULTS 6 events 7 events 7 events 1/C    1/C 
Figure 26.15c
TECHNIQUE 3
1/C  

1/C 
 
1/C
  
1/C
1/C 4
3/A
2/T
3/A  

2/T
3/A
4/C 
 
4/C
4/C
2/T
  
3/A
4/C
2/T
4/C
2/T
3/A
Figure Research Method: Applying parsimony to a problem in molecular systematics
RESULTS  
 
 
  
6 events
7 events
7 events

29. Maximum parsimony- The simplest explanation with the fewest evolutionary events.
Species 
Species 
Species  1
Figure Research Method: Applying parsimony to a problem in molecular systematics
Most likely phylogenetic tree:
RESULTS  

6 events

30. Gene Duplications and Gene Families
Gene duplication is easy to spot and is one of the most important mutations because it can lead to new/more genes, providing more opportunities for evolutionary changes
Like homologous genes, duplicated genes can be traced to a common ancestor
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31. Orthologous and Paralogous Genes
Orthologous genes are found in a single copy in the genome and are homologous between species
They can diverge and end up in two (or more) gene pools because of speciation.
Occurs ONLY AFTER speciation (different species)
Orthologous genes are widespread and extend across many varied species.
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32. Speciation with divergence of gene
Figure 26.18a
Formation of orthologous genes:
a product of speciation
Ancestral gene
Ancestral species
Speciation with
divergence of gene
Figure Two types of homologous genes.
Orthologous genes
Species A
Species B

33. Orthologous and Paralogous Genes
Paralogous genes result from gene duplication, so are found in more than one copy in the genome
They can diverge within the clade that carries them and often evolve new functions
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34. Formation of paralogous genes: within a species
Figure 26.18b
Formation of paralogous genes:
within a species
Ancestral gene
Species C
Gene duplication and divergence
Figure Two types of homologous genes.
Paralogous genes
Species C after many generations

36. Molecular Clocks
Biologists can estimate the rate of evolution based on mutation rates of genes.
Molecular clocks are calibrated against branches of known dates from fossil records.
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37. Neutral Theory
Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness.
Most genetic variation in a population is from the work of genetic drift and mutation, but NOT natural selection.
Variation from natural selection is neutral.
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38. Let’s Review!
Bozeman- Phylogenetic Trees

39. If new evidence were uncovered indicating that taxon E in the figure is the sister taxon of a group consisting of taxa D and F, how would this change the phylogeny below?
Answer: c
This question is linked to Concept Check 26.1, question 4. 39

40. Animals that possess homologous structures probably _____.
evolved from the same ancestor
are headed for extinction
by chance had similar mutations in the past
are not related
Answer: a

41. dragonfly wing and penguin flipper dragonfly wing and bat wing
Which of the following pairs are homologous? Which are analogous? *may choose more than one
dragonfly wing and penguin flipper
dragonfly wing and bat wing
bat wing and seal flipper
butterfly wing and bird wing
Answer: neither: a
analogous: b & d
homologous: c & e
Seal flippers and penguin flippers are both derived from vertebrate forelimbs (homologous), but the forelimbs evolved to the flipper shape independently (analogous). 41

42. dragonfly wing and penguin flipper dragonfly wing and bat wing
Which of the following pairs are homologous? Which are analogous? *may choose more than one
dragonfly wing and penguin flipper
dragonfly wing and bat wing
bat wing and seal flipper
butterfly wing and bird wing
Answer: neither: a
analogous: b & d
homologous: c & e
Seal flippers and penguin flippers are both derived from vertebrate forelimbs (homologous), but the forelimbs evolved to the flipper shape independently (analogous). 42

43. Given the DNA sequence data in the table, which phylogenetic tree is the most parsimonious?
Answer: a 43

44. Which of the phylogenetic hypotheses concerning the origin of the three domains has the least amount of supporting data?
Answer: a 44

45. Cladogram Homework
Check your answers!