If you really decide you like phylogenetics... No quiz today! Duke University Bio 202 Kate L. HertweckNote: 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)
Why bother?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) 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 treesCladogram Phylogramhttp://en.wikipedia.org http://artedi.ebc.uu.se Unrooted vs. rooted http://www.bioinf.manchester.ac.uk
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
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? http://razorwire-phylogeny.blogspot.com● Problem: exhaustively searching trees is impossible.● Solution: use a heuristic strategy!
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, its 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 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
Which of the following represent a homoplasious character?1. wings (bats and birds)2. fur (dogs and cats)3. plant carnivory4. 1 and 25. 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 data where you are trying to cluster 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?