phylolecture

No quiz today!

Duke UniversityBio 202Kate L. Hertweck

If you really decide you like phylogenetics...

Note: This is not my back. My Darwin tattoo is on my wrist.

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)

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

Why bother?

Your flu vaccine would be ineffective without phylogenetics (Ferguson and Anderson, 2010, Nature Medicine)

Why bother?

How does it work?

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

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

What term best describes the taxa circled in blue? Yellow? Red?

1. monophyletic

2. paraphyletic

3. polyphyletic

4. none of the above

Trees can be represented in different ways

http://www.utexas.edu

Diversity in phylogenetic trees

http://en.wikipedia.org http://artedi.ebc.uu.se

http://www.bioinf.manchester.ac.uk

Cladogram Phylogram

Unrooted vs. rooted

1. How many tips?2. How many internal nodes?3. Are the numbered nodes monophyletic?

1. 6 tips2. 4 internal nodes3. Yes!

http://carrot.mcb.uconn.edu

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

Reconstructing phylogenetic trees● How complicated can it be?

● Problem: exhaustively searching trees is impossible.

● Solution: use a heuristic strategy!

http://razorwire-phylogeny.blogspot.com

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

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

Assessing confidence in trees● Polytomy: placement of taxa is unresolved

http://carrot.mcb.uconn.edu

Assessing confidence in trees● Polytomy● Homoplasy: uncertainty in tree resulting from

convergent evolution

http://www.palaeontologyonline.com

Assessing confidence in trees● Polytomy

● Homoplasy

● Bootstrap support: resampling from dataset to estimate how much confidence you should have in each node

Commelinales

Zingiberales

Poales

Dasypogonaceae

Arecales

Asparagales

Liliales

Dioscoreales

Pandanales

Petrosaviales

Alismatales

Acorales

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

Practical uses of phylogenetics

● Tree of life– What are relationships

among all living

organisms?

http://datanotshown.blogspot.com

Practical uses of phylogenetics

● Tree of life– What are relationships

among all living

organisms?

– How do traits evolve?

Practical uses of phylogenetics

● Tree of life● Molecular evolution

– Predicting function of unknown genes

http://dx.doi.org/10.6084/m9.figshare.95620

Practical uses of phylogenetics

● Tree of life● Molecular evolution● Applied phylogenetics

– Conservation

http://evolution.berkeley.edu

Practical uses of phylogenetics

● Tree of life● Molecular evolution● Applied phylogenetics

– Conservation

– Epidemiology

http://evolution.berkeley.edu

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

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

Into the future...

● Phylogenomics

● Trees are networks

● Applying to novel data

– Evolution of language

– Any other type of datawhere you are trying tocluster or visualize connections between data!

http://phylonetworks.blogspot.com

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?