SlideShare a Scribd company logo
1 of 27
Download to read offline
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.
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 trees
Cladogram                                                Phylogram




http://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, 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   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 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 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?

More Related Content

What's hot

Phylogenetic Tree, types and Applicantion
Phylogenetic Tree, types and Applicantion Phylogenetic Tree, types and Applicantion
Phylogenetic Tree, types and Applicantion Faisal Hussain
 
Bioinformatica 24-11-2011-t6-phylogenetics
Bioinformatica 24-11-2011-t6-phylogeneticsBioinformatica 24-11-2011-t6-phylogenetics
Bioinformatica 24-11-2011-t6-phylogeneticsProf. Wim Van Criekinge
 
PhoenixBio 2020 Stanford Workshop on PhyloGenes
PhoenixBio 2020 Stanford Workshop on PhyloGenesPhoenixBio 2020 Stanford Workshop on PhyloGenes
PhoenixBio 2020 Stanford Workshop on PhyloGenesPhoenix Bioinformatics
 

What's hot (7)

Phylogenetic Tree, types and Applicantion
Phylogenetic Tree, types and Applicantion Phylogenetic Tree, types and Applicantion
Phylogenetic Tree, types and Applicantion
 
Phylogenetics
PhylogeneticsPhylogenetics
Phylogenetics
 
Phylogenetic data analysis
Phylogenetic data analysisPhylogenetic data analysis
Phylogenetic data analysis
 
Bioinformatica 24-11-2011-t6-phylogenetics
Bioinformatica 24-11-2011-t6-phylogeneticsBioinformatica 24-11-2011-t6-phylogenetics
Bioinformatica 24-11-2011-t6-phylogenetics
 
PhoenixBio 2020 Stanford Workshop on PhyloGenes
PhoenixBio 2020 Stanford Workshop on PhyloGenesPhoenixBio 2020 Stanford Workshop on PhyloGenes
PhoenixBio 2020 Stanford Workshop on PhyloGenes
 
phylogenetic analysis.pptx
phylogenetic analysis.pptxphylogenetic analysis.pptx
phylogenetic analysis.pptx
 
Parsimony methods
Parsimony methodsParsimony methods
Parsimony methods
 

Viewers also liked

Phylogenetics in R
Phylogenetics in RPhylogenetics in R
Phylogenetics in Rschamber
 
Phylogeny in R - Bianca Santini Sheffield R Users March 2015
Phylogeny in R - Bianca Santini Sheffield R Users March 2015Phylogeny in R - Bianca Santini Sheffield R Users March 2015
Phylogeny in R - Bianca Santini Sheffield R Users March 2015Paul Richards
 
Bayesian phylogenetic inference_big4_ws_2016-10-10
Bayesian phylogenetic inference_big4_ws_2016-10-10Bayesian phylogenetic inference_big4_ws_2016-10-10
Bayesian phylogenetic inference_big4_ws_2016-10-10FredrikRonquist
 
Introduction to Bayesian Phylogenetics
Introduction to Bayesian PhylogeneticsIntroduction to Bayesian Phylogenetics
Introduction to Bayesian PhylogeneticsTracy Heath
 
Bayesian Divergence Time Estimation – Workshop Lecture
Bayesian Divergence Time Estimation – Workshop LectureBayesian Divergence Time Estimation – Workshop Lecture
Bayesian Divergence Time Estimation – Workshop LectureTracy Heath
 
Extra-oral Radiology Techniques I
Extra-oral Radiology Techniques IExtra-oral Radiology Techniques I
Extra-oral Radiology Techniques IIAU Dent
 
Phylogenetics Analysis in R
Phylogenetics Analysis in RPhylogenetics Analysis in R
Phylogenetics Analysis in RKlaus Schliep
 

Viewers also liked (9)

Phylogenetics in R
Phylogenetics in RPhylogenetics in R
Phylogenetics in R
 
Phylogeny in R - Bianca Santini Sheffield R Users March 2015
Phylogeny in R - Bianca Santini Sheffield R Users March 2015Phylogeny in R - Bianca Santini Sheffield R Users March 2015
Phylogeny in R - Bianca Santini Sheffield R Users March 2015
 
Bayesian phylogenetic inference_big4_ws_2016-10-10
Bayesian phylogenetic inference_big4_ws_2016-10-10Bayesian phylogenetic inference_big4_ws_2016-10-10
Bayesian phylogenetic inference_big4_ws_2016-10-10
 
Introduction to Bayesian Phylogenetics
Introduction to Bayesian PhylogeneticsIntroduction to Bayesian Phylogenetics
Introduction to Bayesian Phylogenetics
 
Bayesian Divergence Time Estimation – Workshop Lecture
Bayesian Divergence Time Estimation – Workshop LectureBayesian Divergence Time Estimation – Workshop Lecture
Bayesian Divergence Time Estimation – Workshop Lecture
 
Extra-oral Radiology Techniques I
Extra-oral Radiology Techniques IExtra-oral Radiology Techniques I
Extra-oral Radiology Techniques I
 
Phylogenetic analysis
Phylogenetic analysisPhylogenetic analysis
Phylogenetic analysis
 
Phylogenetics Analysis in R
Phylogenetics Analysis in RPhylogenetics Analysis in R
Phylogenetics Analysis in R
 
Extraoral radiography
Extraoral radiographyExtraoral radiography
Extraoral radiography
 

Similar to Phylolecture

Methods of illustrating evolutionary relationship
Methods of illustrating evolutionary relationshipMethods of illustrating evolutionary relationship
Methods of illustrating evolutionary relationshipEmaSushan
 
MIB200A at UCDavis Module: Microbial Phylogeny; Class 2
MIB200A at UCDavis Module: Microbial Phylogeny; Class 2MIB200A at UCDavis Module: Microbial Phylogeny; Class 2
MIB200A at UCDavis Module: Microbial Phylogeny; Class 2Jonathan Eisen
 
Basics of constructing Phylogenetic tree.ppt
Basics of constructing Phylogenetic tree.pptBasics of constructing Phylogenetic tree.ppt
Basics of constructing Phylogenetic tree.pptSehrishSarfraz2
 
Bls 303 l1.phylogenetics
Bls 303 l1.phylogeneticsBls 303 l1.phylogenetics
Bls 303 l1.phylogeneticsBruno Mmassy
 
Topic 7 Phylogeny.ppt
Topic 7 Phylogeny.pptTopic 7 Phylogeny.ppt
Topic 7 Phylogeny.pptNanda508387
 
Phylogenetic tree construction step by step
Phylogenetic tree construction step by stepPhylogenetic tree construction step by step
Phylogenetic tree construction step by stepShamiGurav1
 
BTC 506 Phylogenetic Tree.pptx
BTC 506 Phylogenetic Tree.pptxBTC 506 Phylogenetic Tree.pptx
BTC 506 Phylogenetic Tree.pptxChijiokeNsofor
 
Uberon EBI industry workshop
Uberon EBI industry workshopUberon EBI industry workshop
Uberon EBI industry workshopChris Mungall
 
Multiple Sequence Alignment-just glims of viewes on bioinformatics.
 Multiple Sequence Alignment-just glims of viewes on bioinformatics. Multiple Sequence Alignment-just glims of viewes on bioinformatics.
Multiple Sequence Alignment-just glims of viewes on bioinformatics.Arghadip Samanta
 
Computational phylogenetics theoretical concepts, methods with practical on C...
Computational phylogenetics theoretical concepts, methods with practical on C...Computational phylogenetics theoretical concepts, methods with practical on C...
Computational phylogenetics theoretical concepts, methods with practical on C...ZarlishAttique1
 
Plant Pathogen Genome Data: My Life In Sequences
Plant Pathogen Genome Data: My Life In SequencesPlant Pathogen Genome Data: My Life In Sequences
Plant Pathogen Genome Data: My Life In SequencesLeighton Pritchard
 
Phylogenetic Tree, types and Applicantion
Phylogenetic Tree, types and Applicantion Phylogenetic Tree, types and Applicantion
Phylogenetic Tree, types and Applicantion Faisal Hussain
 
Processes of Evolution Gibellini
Processes of Evolution GibelliniProcesses of Evolution Gibellini
Processes of Evolution Gibelliningibellini
 
phylogenetictreeanditsconstructionandphylogenyof-191208102256.pdf
phylogenetictreeanditsconstructionandphylogenyof-191208102256.pdfphylogenetictreeanditsconstructionandphylogenyof-191208102256.pdf
phylogenetictreeanditsconstructionandphylogenyof-191208102256.pdfalizain9604
 
Phylogenetic tree and its construction and phylogeny of
Phylogenetic tree and its construction and phylogeny ofPhylogenetic tree and its construction and phylogeny of
Phylogenetic tree and its construction and phylogeny ofbhavnesthakur
 

Similar to Phylolecture (20)

phylogenetic tree.pptx
phylogenetic tree.pptxphylogenetic tree.pptx
phylogenetic tree.pptx
 
Phylogeny-Abida.pptx
Phylogeny-Abida.pptxPhylogeny-Abida.pptx
Phylogeny-Abida.pptx
 
Methods of illustrating evolutionary relationship
Methods of illustrating evolutionary relationshipMethods of illustrating evolutionary relationship
Methods of illustrating evolutionary relationship
 
MIB200A at UCDavis Module: Microbial Phylogeny; Class 2
MIB200A at UCDavis Module: Microbial Phylogeny; Class 2MIB200A at UCDavis Module: Microbial Phylogeny; Class 2
MIB200A at UCDavis Module: Microbial Phylogeny; Class 2
 
Basics of constructing Phylogenetic tree.ppt
Basics of constructing Phylogenetic tree.pptBasics of constructing Phylogenetic tree.ppt
Basics of constructing Phylogenetic tree.ppt
 
Bls 303 l1.phylogenetics
Bls 303 l1.phylogeneticsBls 303 l1.phylogenetics
Bls 303 l1.phylogenetics
 
Topic 7 Phylogeny.ppt
Topic 7 Phylogeny.pptTopic 7 Phylogeny.ppt
Topic 7 Phylogeny.ppt
 
Phylogenetic tree construction step by step
Phylogenetic tree construction step by stepPhylogenetic tree construction step by step
Phylogenetic tree construction step by step
 
BTC 506 Phylogenetic Tree.pptx
BTC 506 Phylogenetic Tree.pptxBTC 506 Phylogenetic Tree.pptx
BTC 506 Phylogenetic Tree.pptx
 
Uberon EBI industry workshop
Uberon EBI industry workshopUberon EBI industry workshop
Uberon EBI industry workshop
 
Multiple Sequence Alignment-just glims of viewes on bioinformatics.
 Multiple Sequence Alignment-just glims of viewes on bioinformatics. Multiple Sequence Alignment-just glims of viewes on bioinformatics.
Multiple Sequence Alignment-just glims of viewes on bioinformatics.
 
phylogenetics.pdf
phylogenetics.pdfphylogenetics.pdf
phylogenetics.pdf
 
07_Phylogeny_2022.pdf
07_Phylogeny_2022.pdf07_Phylogeny_2022.pdf
07_Phylogeny_2022.pdf
 
Computational phylogenetics theoretical concepts, methods with practical on C...
Computational phylogenetics theoretical concepts, methods with practical on C...Computational phylogenetics theoretical concepts, methods with practical on C...
Computational phylogenetics theoretical concepts, methods with practical on C...
 
Plant Pathogen Genome Data: My Life In Sequences
Plant Pathogen Genome Data: My Life In SequencesPlant Pathogen Genome Data: My Life In Sequences
Plant Pathogen Genome Data: My Life In Sequences
 
Phylogenetic Tree, types and Applicantion
Phylogenetic Tree, types and Applicantion Phylogenetic Tree, types and Applicantion
Phylogenetic Tree, types and Applicantion
 
Processes of Evolution Gibellini
Processes of Evolution GibelliniProcesses of Evolution Gibellini
Processes of Evolution Gibellini
 
phylogenetictreeanditsconstructionandphylogenyof-191208102256.pdf
phylogenetictreeanditsconstructionandphylogenyof-191208102256.pdfphylogenetictreeanditsconstructionandphylogenyof-191208102256.pdf
phylogenetictreeanditsconstructionandphylogenyof-191208102256.pdf
 
Phylogenetic tree and its construction and phylogeny of
Phylogenetic tree and its construction and phylogeny ofPhylogenetic tree and its construction and phylogeny of
Phylogenetic tree and its construction and phylogeny of
 
Hertweck uva2012
Hertweck uva2012Hertweck uva2012
Hertweck uva2012
 

More from Kate Hertweck

Opening science to interdisciplinarity: balancing trade-offs while creating, ...
Opening science to interdisciplinarity: balancing trade-offs while creating, ...Opening science to interdisciplinarity: balancing trade-offs while creating, ...
Opening science to interdisciplinarity: balancing trade-offs while creating, ...Kate Hertweck
 
Archives of a Future Commons: Seeds and/as Data
Archives of a Future Commons:  Seeds and/as DataArchives of a Future Commons:  Seeds and/as Data
Archives of a Future Commons: Seeds and/as DataKate Hertweck
 
Hertweck Evolution 2017
Hertweck Evolution 2017Hertweck Evolution 2017
Hertweck Evolution 2017Kate Hertweck
 
Hertweck AB3ACBS presentation
Hertweck AB3ACBS presentationHertweck AB3ACBS presentation
Hertweck AB3ACBS presentationKate Hertweck
 
Transposable elements of Agavoideae
Transposable elements of AgavoideaeTransposable elements of Agavoideae
Transposable elements of AgavoideaeKate Hertweck
 
Developing an undergraduate bioinformatics course
Developing an undergraduate bioinformatics courseDeveloping an undergraduate bioinformatics course
Developing an undergraduate bioinformatics courseKate Hertweck
 
Evolution of transposons, genomes, and organisms (Hertweck Fall 2014)
Evolution of transposons, genomes, and organisms (Hertweck Fall 2014)Evolution of transposons, genomes, and organisms (Hertweck Fall 2014)
Evolution of transposons, genomes, and organisms (Hertweck Fall 2014)Kate Hertweck
 
Hertweck Evolution 2014
Hertweck Evolution 2014Hertweck Evolution 2014
Hertweck Evolution 2014Kate Hertweck
 
Hertweck Monocots V Presentation
Hertweck Monocots V PresentationHertweck Monocots V Presentation
Hertweck Monocots V PresentationKate Hertweck
 
Hertweck Asparagales 2013
Hertweck Asparagales  2013Hertweck Asparagales  2013
Hertweck Asparagales 2013Kate Hertweck
 
iEvoBio Hertweck abstract 2012
iEvoBio Hertweck abstract 2012iEvoBio Hertweck abstract 2012
iEvoBio Hertweck abstract 2012Kate Hertweck
 
iEvoBio Hertweck presentation 2012
iEvoBio Hertweck presentation 2012iEvoBio Hertweck presentation 2012
iEvoBio Hertweck presentation 2012Kate Hertweck
 

More from Kate Hertweck (15)

Opening science to interdisciplinarity: balancing trade-offs while creating, ...
Opening science to interdisciplinarity: balancing trade-offs while creating, ...Opening science to interdisciplinarity: balancing trade-offs while creating, ...
Opening science to interdisciplinarity: balancing trade-offs while creating, ...
 
Archives of a Future Commons: Seeds and/as Data
Archives of a Future Commons:  Seeds and/as DataArchives of a Future Commons:  Seeds and/as Data
Archives of a Future Commons: Seeds and/as Data
 
Hertweck Evolution 2017
Hertweck Evolution 2017Hertweck Evolution 2017
Hertweck Evolution 2017
 
Hertweck AB3ACBS presentation
Hertweck AB3ACBS presentationHertweck AB3ACBS presentation
Hertweck AB3ACBS presentation
 
Transposable elements of Agavoideae
Transposable elements of AgavoideaeTransposable elements of Agavoideae
Transposable elements of Agavoideae
 
Careers in Botany
Careers in BotanyCareers in Botany
Careers in Botany
 
Developing an undergraduate bioinformatics course
Developing an undergraduate bioinformatics courseDeveloping an undergraduate bioinformatics course
Developing an undergraduate bioinformatics course
 
Evolution of transposons, genomes, and organisms (Hertweck Fall 2014)
Evolution of transposons, genomes, and organisms (Hertweck Fall 2014)Evolution of transposons, genomes, and organisms (Hertweck Fall 2014)
Evolution of transposons, genomes, and organisms (Hertweck Fall 2014)
 
Hertweck Evolution 2014
Hertweck Evolution 2014Hertweck Evolution 2014
Hertweck Evolution 2014
 
Hertweck Monocots V Presentation
Hertweck Monocots V PresentationHertweck Monocots V Presentation
Hertweck Monocots V Presentation
 
Hertweck Asparagales 2013
Hertweck Asparagales  2013Hertweck Asparagales  2013
Hertweck Asparagales 2013
 
Hertweck bbl2012
Hertweck bbl2012Hertweck bbl2012
Hertweck bbl2012
 
iEvoBio Hertweck abstract 2012
iEvoBio Hertweck abstract 2012iEvoBio Hertweck abstract 2012
iEvoBio Hertweck abstract 2012
 
iEvoBio Hertweck presentation 2012
iEvoBio Hertweck presentation 2012iEvoBio Hertweck presentation 2012
iEvoBio Hertweck presentation 2012
 
Evolution 2012
Evolution 2012Evolution 2012
Evolution 2012
 

Phylolecture

  • 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?