1. 5.4 Cladistics

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 ancestor 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. 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!)

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

10. 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

11. 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

12. Cladistics and Phylogeny
Cladistics uses the presence or absence of derived traits (recently evolved traits) to determine how closely related two groups or organisms are.
If they share a derived trait, they are thought to be more closely related to each other.

13. Cladograms and Phylogenetic Trees
These are diagrams used to show the evolutionary relationship between organisms.
The terms may be used interchangeably however:
Cladograms use morphological evidence and Phylogenetic Trees you genetic sequences (DNA, RNA, mDNA)

14. Species A is the most recent common ancestor shared by all groups
Species B is a common ancestor to all groups except the ray-finned fish
The most common ancestor of a mammal and a dinosaur is Species C

15. Morphological Traits vs Genes?
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.

16. 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.

17. 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

18. 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

19. 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.

21. Analysis of Cladograms
Note: Although cladograms provide strong evidence for the evolutionary history of a group, they cannot be regarded as infallible proof
Cladograms are constructed on the assumption that the smallest possible number of mutations occurred to account for current base or amino acid sequence
Sometimes the assumptions made by cladograms are incorrect.
It’s best to compare several versions produced by using different genes/traits

22. Reclassification
Evidence from cladistics has led to the renaming and the regrouping of organisms.
Occasionally organisms long thought to be related because of shared physical traits are reclassified based on phylogenetic trees constructed from biochemical evidence.

23. Evidence from traditional cladistics has shown that classification of some groups based on morphology does not correspond with the evolutionary origins of a group of species.

24. Cladograms and falsification
Falsification of theories with one theory being superseded by another has been observed from the reclassification of plants as a result of evidence from cladistics.
The classification of angiosperms into families based on their morphology was begun by French botanist Antoine Laurent de Jussieu in 1789, and was revised repeatedly during the 19th century.

25. Classification of the figwort family
Until recently, Figworts (Scrophulariaceae family) were the 8th largest family of angiosperms (flowering plants).
It was one of the original families proposed by de Jussieu in As more plants were discovered, the family grew from 16 genera in 1789 (based on similarities in their morphology) to 275 genera, with more than 5,000 species.

26. Classification of the figwort family
Taxonomists recently examined the base sequences of three chloroplast genes and found that the 5000 figwort species were not a true clade and that 5 clades had incorrectly been combined into one family.
Less than half of the original species remain in the Figwort family; now only the 36th largest among angiosperms.
Reclassification was helpful since old Figwort family was too large and dissimilar to be a helpful grouping.

27. Scrophulara peregrina has remained in the figwort family.
Antirrhinum majus has been transferred from the figwort family to the plantain family.
Scrophulara peregrina has remained in the figwort family.

28. 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.

29. 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

30. 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.

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

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

34. How to make a cladogram

35. Constructing a Cladogram

42. Exit Card
Draw a cladogram based on the following information:

43. Answer: