1. Phylogenetics https://youtu.be/fQwI90bkJl4
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Model of sequence evolution
Phylogenetic trees and networks
Cladistic and phenetic methods
Computer software and demos
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy

2. Phylogenetic Inference I
Recommended readings
A science primer: Phylogenetics
Brown, S.M. (2000) Bioinformatics, Eaton Publishing, pp
Brown, S.M.: Molecular Phylogenetics
Hillis, D.M.; Moritz, G. & Mable, B.K. (1996) Molecular Systematics, Edition, Sinauer Associates, 655 pp.
Mount, D.W. (2001) Bioinformatics, Cold Spring Harbor Lab Press, pp
(very) basic
advanced
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy

3. Classifying Organisms
Nomenclature is the science of naming organisms
Evolution has created an enormous diversity, so how do we deal with it?
Names allow us to talk about groups of organisms.
- Scientific names were originally descriptive phrases; not practical
- Binomial nomenclature
> Developed by Linnaeus, a Swedish naturalist
> Names are in Latin, formerly the language of science
> binomials - names consisting of two parts
> The generic name is a noun.
> The epithet is a descriptive adjective.
- Thus a species' name is two words e.g. Homo sapiens
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy
Carolus Linnaeus ( )

4. Classifying Organisms
Taxonomy is the science of the classification of organisms
Taxonomy deals with the naming and ordering of taxa.
The Linnaean hierarchy:
1. Kingdom
2. Division
3. Class
4. Order
5. Family
6. Genus
7. Species
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy
Evolutionary distance

5. Classifying Organisms
Systematics is the science of the relationships of organisms
Systematics is the science of how organisms are related and the evidence for those relationships
Systematics is divided primarily into phylogenetics and taxonomy
Speciation -- the origin of new species from previously existing ones
- anagenesis - one species changes into another over time
- cladogenesis - one species splits to make two
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy
Reconstruct evolutionary history
Phylogeny

6. Phylogenetics
Phylogenetics is the science of the pattern of evolution.
A. Evolutionary biology is the study of the processes that generate diversity, while phylogenetics is the study of the pattern of diversity produced by
those processes.
B. The central problem of phylogenetics:
1. How do we determine the relationships between species?
2. Use evidence from shared characteristics, not differences
3. Use homologies, not analogies
4. Use derived condition, not ancestral
a. synapomorphy - shared derived characteristic
b. plesiomorphy - ancestral characteristic
C. Cladistics is phylogenetics based on synapomorphies.
1. Cladistic classification creates and names taxa based only on synapomorphies.
2. This is the principle of monophyly
3. monophyletic, paraphyletic, polyphyletic
4. Cladistics is now the preferred approach to phylogeny
Review of protein structures
Need for analyses of protein structures
Sources of protein structure information
Computational Modeling
DNA/RNA overview
The phylogeny and classification of life as proposed by Haeckel (1866)

7. Phylogenetics
Evolutionary theory states that groups of similar organisms are descended from a common ancestor.
Phylogenetic systematics is a method of taxonomic classification based on their evolutionary history.
It was developed by Hennig, a German entomologist, in 1950.
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy
Willi Hennig ( )

8. Phylogenetics Phylogenetics is the science of the pattern of evolution
Evolutionary biology versus phylogenetics
- Evolutionary biology is the study of the processes that generate diversity
- Phylogenetics is the study of the pattern of diversity produced by those processes
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy

9. Phylogenetics Who uses phylogenetics? Some examples:
Evolutionary biologists (e.g. reconstructing tree of life)
Systematists (e.g. classification of groups)
Anthropologists (e.g. origin of human populations)
Forensics (e.g. transmission of HIV virus to a rape victim)
Parasitologists (e.g. phylogeny of parasites, co-evolution)
Epidemiologists (e.g. reconstruction of disease transmission)
Genomics/Proteomics (e.g. homology comparison of new proteins)
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy

10. Phylogenetic trees The central problem of phylogenetics:
how do we determine the relationships between taxa?
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy
in phylogenetic studies, the most convenient way of presenting evolutionary relationships among a group of organisms is the phylogenetic tree

11. Phylogenetics
Phylogenetics is the science of the pattern of evolution.
A. Evolutionary biology is the study of the processes that generate diversity, while phylogenetics is the study of the pattern of diversity produced by
those processes.
B. The central problem of phylogenetics:
1. How do we determine the relationships between species?
2. Use evidence from shared characteristics, not differences
3. Use homologies, not analogies
4. Use derived condition, not ancestral
a. synapomorphy - shared derived characteristic
b. plesiomorphy - ancestral characteristic
C. Cladistics is phylogenetics based on synapomorphies.
1. Cladistic classification creates and names taxa based only on synapomorphies.
2. This is the principle of monophyly
3. monophyletic, paraphyletic, polyphyletic
4. Cladistics is now the preferred approach to phylogeny
Review of protein structures
Need for analyses of protein structures
Sources of protein structure information
Computational Modeling
DNA/RNA overview

12. Phylogenetic trees
Node: a branchpoint in a tree (a presumed ancestral OTU)
Branch: defines the relationship between the taxa in terms of descent and ancestry
Topology: the branching patterns of the tree
Branch length (scaled trees only): represents the number of changes that have occurred in the branch
Root: the common ancestor of all taxa
Clade: a group of two or more taxa or DNA sequences that includes both their common ancestor and all their descendents
Operational Taxonomic Unit (OTU): taxonomic level of sampling selected by the user to be used in a study, such as individuals, populations, species, genera, or bacterial strains
Branch
DNA/RNA overview
Node
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy
Clade
Root

13. Phylogenetic trees There are many ways of drawing a tree
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy

14. = = Phylogenetic trees There are many ways of drawing a tree E D C B A
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy

15. = = Phylogenetic trees There are many ways of drawing a tree
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy
no meaning

16. = / Phylogenetic trees There are many ways of drawing a tree
Bifurcation
Trifurcation
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy
Bifurcation versus Multifurcation (e.g. Trifurcation)
Multifurcation (also called polytomy): a node in a tree that connects more than three branches. A multifurcation may represent a lack of resolution because of too few data available for inferring the phylogeny (in which case it is said to be a soft multifurcation) or it may represent the hypothesized simultaneous splitting of several lineages (in which case it is said to be a hard multifurcation).

17. Phylogenetic trees
Trees can be scaled or unscaled (with or without branch lengths)
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy

18. Phylogenetic trees Trees can be unrooted or rooted D A C B A C B D A C
Unrooted tree A C B D
Root
Rooted tree
Root
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy A C B D
Root D A C B
Root

19. Phylogenetic trees Trees can be unrooted or rooted
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy
These trees show five different evolutionary relationships among the taxa!

20. Phylogenetic trees Possible evolutionary trees Taxa (n): 2 3 4
Unrooted/rooted
2 1/1
3 1/3
4 3/15
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy

21. Phylogenetic trees Possible evolutionary trees Taxa (n) rooted
(2n-3)!/(2n-2(n-2)!)
unrooted
(2n-5)!/(2n-3(n-3)!) 2 1 3 4 15 5
105 6
954 7
10,395 8
135,135 9
2,027,025 10
34,459,425
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy

22. Phylogenetic trees How to root? Use information from ancestors
DNA/RNA overview
In most cases not available
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy

23. Phylogenetic trees How to root?
Use statistical tools will root trees automatically (e.g. mid-point rooting)
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy
This must involve assumptions … BEWARE!

24. Phylogenetic trees How to root? Using “outgroups” DNA/RNA overview
- the outgroup should be a taxon known to be less closely related to the rest of the taxa (ingroups)
- it should ideally be as closely related as possible to the rest of the taxa while still satisfying the above condition
Using “outgroups”
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy

25. Phylogenetic trees Exercise: rooted/unrooted; scaled/unscaled A B C D
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Homology and homoplasy D E F

26. Phylogenetics What are useful characters? Cactaceae
Use homologies, not analogies!
Homology: common ancestry of two or more character states
Analogy: similarity of character states not due to shared ancestry
- Homoplasy: a collection of phenomena that leads to similarities in character states for reasons other than inheritance from a common ancestor (e.g. convergence, parallelism, reversal)
Homoplasy is huge problem in morphology data sets!
But in molecular data sets, too!
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Homology and homoplasy
Cladistic versus phenetic analyses
Cactaceae
(cactus spines are modified leaves)
Euphorbiaceae (euphorb spines are modified shoots)

27. Phylogenetics Molecular data and homoplasy
gene sequences represent character data
characters are positions in the sequence (not all workers agree; some say one gene is one character)
character states are the nucleotides in the sequence (or amino acids in the case of proteins)
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Homology and homoplasy
Cladistic versus phenetic analyses
Problems:
the probability that two nucleotides are the same just by chance mutation is 25%
what to do with insertions or deletions (which may themselves be characters)
homoplasy in sequences may cause alignment errors

28. Phylogenetics Molecular data and homoplasy: Orthologs vs. Paralogs
When comparing gene sequences, it is important to distinguish between identical vs. merely similar genes in different organisms
Orthologs are homologous genes in different species with analogous functions
Paralogs are similar genes that are the result of a gene duplication
A phylogeny that includes both orthologs and paralogs is likely to be incorrect
Sometimes phylogenetic analysis is the best way to determine if a new gene is an ortholog or paralog to other known genes
DNA/RNA overview
Taxonomy and phylogenetics
Phylogenetic trees
Homology and homoplasy
Cladistic versus phenetic analyses

29. Phenetics versus cladistics
Within the field of taxonomy there are two different methods and philosophies of building phylogenetic trees: cladistic and phenetic
Phenetic methods construct trees (phenograms) by considering the current states of characters without regard to the evolutionary history that brought the species to their current phenotypes; phenograms are based on overall similarity
Cladistic methods construct trees (cladograms) rely on assumptions about ancestral relationships as well as on current data; cladograms are based on character evolution (e.g. shared derived characters)
Cladistics is becoming the method of choice; it is considered to be more powerful and to provide more realistic estimates, however, it is slower than phenetic algorithms

30. Phenetics vs. cladistics
An example

31. Phenetics vs. cladistics
Phenetic (overall similarity)
overall similarity 3 4 5 A B C

32. Phenetics vs. cladistics
Cladistics (character evolution; e.g. shared derived characters)
shared derived characters 1 2 A B C