Phylogenetics is the study of evolutionary relationships among groups of organisms. A phylogenetic tree represents these relationships, showing how groups are hierarchically related through hypothetical common ancestors. Building phylogenies involves obtaining data, determining homology, and using software to construct the tree based on optimality criteria like parsimony or likelihood. Phylogenies have many practical uses like understanding the tree of life, molecular evolution, conservation, and epidemiology. Future directions include phylogenomics using genome-wide data and considering trees as networks rather than hierarchies.

1. If you really decide you like phylogenetics...
No quiz today!
Duke University
Bio 202
Kate L. Hertweck
Note: This is not my back.
My Darwin tattoo is on my wrist.

2. The main idea of phylogenetics
● A phylogenetic tree (phylogeny) represents evolutionary
relationships among a group
– Hierarchical in nature
– Group may consist of species, genes, families, etc
● How to do it:
– Obtain data
– Decide on homology (common evolutionary origin, multiple
sequence alignment)
– Build phylogeny (many kinds of software available)

3. Why bother?
Phylogenetic evidence is vital in criminal cases of HIV
transmission (Scaduto et al., 2010, PNAS)

4. Why bother?
Your flu vaccine would be
ineffective without
phylogenetics (Ferguson
and Anderson, 2010,
Nature Medicine)
How does it work?

5. Parts of a phylogeny
● Leaves (tips): individually sampled units in the tree (current day
species)
● Nodes: hypothetical common ancestors
● Branches (internodes, edges): time or changes from one node to the
next
● Outgroup: a close relative to tips of interest, which diverges earlier
and serves as a reference point
http://arthropoda.wordpress.com

6. Describing a phylogeny
● Monophyletic (clade): group of leaves descended from a
common ancestor
● Paraphyletic: a group including not all leaves descended
from a common ancestor
● Polyphyletic: a group including leaves from multiple clades
http://www.oglethorpe.edu

7. What term best describes the taxa
circled in blue? Yellow? Red?
1. monophyletic
2. paraphyletic
3. polyphyletic
4. none of the above

8. Trees can be represented in different ways
http://www.utexas.edu

9. Diversity in phylogenetic trees
Cladogram Phylogram
http://en.wikipedia.org http://artedi.ebc.uu.se
Unrooted vs. rooted
http://www.bioinf.manchester.ac.uk

10. 1. How many tips?
2. How many internal nodes?
3. Are the numbered nodes monophyletic?
1. 6 tips
2. 4 internal nodes
3. Yes!
http://carrot.mcb.uconn.edu

11. What data are used to build
phylogenies?
● Morphology: presence/absence of organism parts,
number of legs, color, etc. (can include fossils!)
● Molecules (genetic data): DNA, protein, gene order
– Organellar DNA is uniparentally inherited
– Nuclear DNA is biparentally inherited
– Ancient DNA (from long extinct organisms)
● Gene trees vs. species trees

12. Reconstructing phylogenetic trees
● How complicated can it be?
http://razorwire-phylogeny.blogspot.com
● Problem: exhaustively searching trees is
impossible.
● Solution: use a heuristic strategy!

13. Optimality criteria: Which tree is the best?
● Minimum evolution (distance): tree with shortest length
(in number of morphological or nucleotide changes) is
preferred
– Data transformed into pairwise similarity matrix
– Only indirectly implies evolutionary relatedness
● Parsimony: the simplest answer is preferred (tree with
fewest steps to represent differences between taxa)
– Minimize number of evolutionary events along tree
branches
● Model-based methods: apply a model of evolution
● Note: Distance and parsimony indirectly apply a
“model” of evolution, it's just inherent in the algorithm

14. Models of evolution (usually sequence data)
● Maximum likelihood (and Bayesian inference)
● Tree with higher probability of giving rise to the data is
preferred
● Substitution models: each site is a position in a sequence,
model describes how sites evolve
– Range from very simple (substitution rates and all other
parameters are equal) to very complex (sites evolve at
different rates)
– Separate models for DNA, protein, and other data types

15. Assessing confidence in trees
● Polytomy: placement of taxa is unresolved
http://carrot.mcb.uconn.edu

16. Assessing confidence in trees
● Polytomy
● Homoplasy: uncertainty in tree resulting from
convergent evolution
http://www.palaeontologyonline.com

17. Assessing confidence in trees
● Polytomy
● Homoplasy
● Bootstrap support: resampling Commelinales
from dataset to estimate Zingiberales
how much confidence you Poales
Dasypogonaceae
should have in each node
Arecales
Asparagales
Liliales
Dioscoreales
Pandanales
Petrosaviales
Alismatales
Acorales

18. Which of the following represent a
homoplasious character?
1. wings (bats and birds)
2. fur (dogs and cats)
3. plant carnivory
4. 1 and 2
5. 1, 2 and 3

19. Practical uses of phylogenetics
● Tree of life
– What are relationships
among all living
organisms?
http://datanotshown.blogspot.com

20. Practical uses of phylogenetics
● Tree of life
– What are relationships
among all living
organisms?
– How do traits evolve?

21. Practical uses of phylogenetics
● Tree of life
● Molecular evolution
– Predicting function of unknown genes
http://dx.doi.org/10.6084/m9.figshare.95620

22. Practical uses of phylogenetics
● Tree of life
● Molecular evolution
● Applied phylogenetics
– Conservation
http://evolution.berkeley.edu

23. Practical uses of phylogenetics
● Tree of life
● Molecular evolution
● Applied phylogenetics
– Conservation
– Epidemiology
http://evolution.berkeley.edu

24. Into the future...
● Phylogenomics
– Obtain genome-wide sequence data for many species
– Evaluate evolutionary history of gene families, as
informed by species phylogeny
http://www.scilifelab.se

25. Into the future...
● Phylogenomics
● Trees are networks
– Historical events may cause
reticulation in the tree
– Hybridization, gene flow
McDonald D B et al. PNAS 2008;105:10837-10842

26. Into the future...
● Phylogenomics
● Trees are networks
● Applying to novel data
– Evolution of language
– Any other type of data
where you are trying to
cluster or visualize
connections between
data!
http://phylonetworks.blogspot.com

27. Conclusions
● Phylogenetics allows us to infer past
evolutionary events
● Powerful tool for empirical and applied
purposes
● Allows inference of trait evolution, with some
predictive power
● Questions?