1. Phylogeny and the Tree of Life
Chapter 26

2. YOU MUST KNOW
The taxonomic categories and how they indicate relatedness
How systematics is used to develop phylogenetic trees
How to construct a phylogenetic tree that represents processes of biological evolution
The three domains of life, including their similarities and their differences
The significance of widely conserved processes across the three domains

3. I. Phylogeny
The evolutionary history of a species or group of related species
Systematics-classifying organisms and their evolutionary relationships
1. Uses fossils, morphology, genes and molecular evidence
Domains est. 1990

4. C. Taxonomy – division of organisms into categories based on similarities and differences 1. Binomial nomenclature – two part naming system (genus and species) developed by Carolus Linnaeus)
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5. The lower in this hierarchy that two species share a classification, to more closely related they are

6. 1. Divergences indicate common ancestors
Phylogenetic trees – depict hypotheses about evolutionary relationships
1. Divergences indicate common ancestors
Be aware this unit introduces a lot of vocabulary such as polytomy. Explain polytomy is understood to be temporary, since the hope is that sometime future evidence will resolve the polytomy. The resolution will determine which group evolved from which group.
Sister taxa are groups or organisms that share an immediate common ancestor. Also note the branches can rotate and still represent the same phylogeny.

7. Rotating Branches Rotating Branches
Emphasize that inverting the diagram top to bottom does not “change” the evolutionary history. The common ancestor remains the same.
The two phylogenetic trees illustrate the same evolutionary relationships. The vertical branches have been rotated.

8. -cat example
-branch tips = extant spp; root = common ancestor; branches = history of descent; node = point where 1 spp split into 2+ descendents
-lynx & bobcat closest relatives, share a more recent common ancestor with each other than with any other spp on the tree; therefore called ‘sister taxa’
-‘taxon’ any named group of organisms, genus, spp, family etc.
-leopard derived with descent with modification from recent ancestors with similar coats and distant ancestors with flecks
-this is a hypothesis!
-we do not know true history, we identify most plausible scenario
-different data sets can produce different trees
-branch lengths arbitrary, arranged to improve readability
-root establishes order of divergence events

9. Which pair is more closely related
Which pair is more closely related? A lizard/crocodile or bird/crocodile?

10. This diagram shows a relationship between 4 relatives
This diagram shows a relationship between 4 relatives. These relatives share a common ancestor at the root of the tree.
Note that this diagram is also a timeline. The older organism is at the bottom of the tree.
Branches on the tree represent SPECIATION, the formation of a new species.
The four descendents at the top of the tree are DIFFERENT species. This is called SPECIATION.

11. Look at the cladogram at the left
Look at the cladogram at the left. What conclusions can be drawn about the relationship between humans and chimps?

12. Species B and C each have characteristics that are unique only to them.
But they also share some part of their history with species A. This shared history is the common ancestor

13. Use morphological and molecular data
1. Must consider homologous structures, convergent evolution and analogous structures, and molecular systematics (DNA, RNA, protein sequence similarities)

14. II. Cladograms
Depict patterns of shared characteristics, basis of phylogenetic trees but does not show time or genetic distance
1. Clade – group of species which includes an ancestral species and all its descendants (monophyletic group)

15. Based on the phylogeny shown, we can conclude that species 2 is most closely related to species ______ 3

16. Shared derived characteristics – evolutionary novelties unique to a clade (ex. hair in mammals)
Shared ancestral characteristics – originated in an ancestor, shared by more than one clade (ex. all mammals have backbones, but so do all vertebrates)

17. Based on the phylogeny shown, the outgroup would be species ______1

19. Making a Cladogram Based on Traits
Examine the data given.
Propose a cladogram depicting the evolutionary history of the vertebrates.
The lancet is an outgroup which is a group that is closely related to the taxa being examined but is less closely related as evidenced by all those zeros!
The taxa being examined is called the ingroup.
Let the students use information in the table and construct a cladogram. Tell the student that using a 1 vs. a 0 is simply one convention with regard to presenting the data. Sometimes + and - are used or perhaps an X and nothing at all in the table.

20. Making a Cladogram Based on Traits
Note that each trait exists only after the group divides into two.
Graphic from Campbell.

21. The cladogram shows the evolution of land plants as indicated by fossil records.
Which discovery would challenge the validity of this cladogram?
A A large aquatic vascular plant about 200 million years old
B A species of algae that has existed for less than one million years
C A moss species that has existed for less than 380 million years
D A fossil of a fern more than 425 million years old D

22. III. Evolutionary History & Genomes
Rate of DNA evolution varies within a genome
DNA that codes for ribosomal RNA changes slowly (useful for examining divergences that happened millions of years ago)
DNA that codes for mitochondrial DNA evolves rapidly (examined for more recent events)

23. B. The molecular clock hypothesis states: Among closely related species, a given gene usually evolves at reasonably constant rate. Used to measure time of evolutionary change based on the rates of genome changes

24. Molecular Clocks
Molecular clocks can be used to study genomes that change rather quickly such as the HIV-1 virus (a retrovirus).
Using a molecular clock, it as been estimated that the HIV-1 virus entered the human population in 1960’s and the origin of the virus dates back to the 1930’s.

25. IV. Taxonomy is frequently revised
A. Switch to 3 Domain system – first introduced in 1977, widely adopted in 1990

26. Membrane bound organelles
Characteristics
Bacteria
Archaea
Eukarya
Nuclear envelope No
Yes
Membrane bound organelles
Introns
Histone proteins associated with DNA
Circular chromosome