1. D.5: Phylogeny and Systematics

2. Classifying Organisms
Systematics / Taxonomy: the study of classifying organisms into groups
The best classification systems categorize organisms based on natural relationships due to common ancestry (homologous features) rather than incidental similarities (analogous features)

3. Homologous vs. Analogous
Homologous Structures: features that are common in different organisms because their common ancestry also possessed this feature.
Ex: pentadactyl limb of humans, cats, bats, whales…..
Analogous Structures: features in different organisms that serve a similar function, however they are structurally different since they evolved independently (their common ancestor does not posses this feature)
Ex: wings of birds, bats, and insects

4. Vestigial Structures
These are structures that do not serve a function in an organism but are believed to have had a purpose in earlier ancestors.
“Evolutionary baggage”
Shows homology
Ex: appendix: While in modern humans there is no purpose, it is believed that it used to aid in the digestion of cellulose when our ancestor’s diets were more plant based.
Ex: Gills in embryos

6. Linnaean Taxonomy
The traditional Linnaean system of taxonomy attempted to classify organisms based on their morphological characteristics
It did not account for analogous structures and convergent evolution
As a result, it does not show true evolutionary relationships

7. Cladistics / Phylogenetics
Attempt to illustrate the evolutionary relationship between organism with phylogenetic trees/ cladograms
Uses morphological characteristics such as homologous structures but not analogous structures
Usually uses biochemical evidence such as DNA, RNA, mDNA (mitochondrial DNA) and protein sequences

8. Biochemical Evidence
How does biochemical evidence support the idea that all living organisms on Earth share a common ancestor?
All organisms use DNA or RNA as their molecule of heredity.
These nucleic acids code for proteins. All organisms use virtually the same 20 amino acids (and in the same conformation – left handed!)

10. The genetic code is universal – all living organisms use the same “codon dictionary” to interpret DNA and code for amino acids

11. Modern evolutionary biologists use biochemical evidence to create phylogenetic trees.
They often use mDNA.
Mitochondrial DNA in all organisms is quite similar. However, the differences can provide insight as to the evolutionary relationships between organisms.

12. Ex: Alpha-Hemoglobin
Analysis of the sequences for the alpha-hemoglobin chain show that:
The sequences or amino acids are identical in humans and in chimps
There are only 2 amino acids that differ in the sequences of orangutans.
This suggests that humans are more closely related to chimps than they are orangutans

13. Phylogenetic Tree
This node represents the common ancestor of a human and a mouse.
The point where the tree branches is called a “node”. This is represents a common ancestor.

14. The alpha-hemoglobin in these 2 ancestral species is different
The alpha-hemoglobin in these 2 ancestral species is different. There are a minimum of 51 substitution mutations between them

15. Phylogenetic trees are usually confirmed by studying other conserved proteins such as cytochrome c (an enzyme essential for cellular respiration), as well as the fossil record and other taxonomic data such as evolutionary clocks

16. Evolutionary Clock
A technique in molecular genetics to date when two species diverged.
It calculates the time since their common ancestry by examining the number of differences between their DNA or protein sequences.
Assumes that the rate of evolutionary change of any protein or DNA sequences is constant over time.

18. Definitions
Cladistics: a method of taxonomy based on constructing groups, or clades comprising organisms which share unique homologous characteristics.
Clade: a group of organisms with a single common ancestor and ALL the descendants of that ancestor.
The group shares common characteristics, or derived characteristics.
Cladogram: diagrams that shows the relationship between clades

19. All 3 of these cladograms show the exact same information
4 present day species are indicated (A, B,C,D)
Node 1: shows a common ancestor to all 4 species

20. Node 3: is only common to C and D
Since species B and C share a more recent common ancestor (node 2) they are more closely related that A and B.

21. Cladistics only recognizes monophyletic groups
MONOPHYLETIC – groups that include a single ancestor and ALL of its descendants.

22. Polyphyletic: groups that do not include a common ancestor
Paraphyletic: groups that include the common ancestor but not all of its descendants

24. How to make a cladogram

25. Constructing a Cladogram