Phylogeny reconstruction
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Phylogeny reconstruction . How do we reconstruct the tree of life? Outline: Terminology Methods distance parsimony maximum likelihood bootstrapping Problems homoplasy hybridisation. Dr. Sean Graham, UBC. . Phylogenetic reconstruction. Phylogenetic reconstruction.

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Phylogeny reconstruction

Phylogeny reconstruction

  • How do we reconstruct the tree of life?

  • Outline:

  • Terminology

  • Methods

  • distance

  • parsimony

  • maximum likelihood

  • bootstrapping

  • Problems

  • homoplasy

  • hybridisation

Dr. Sean Graham, UBC.


Phylogeny reconstruction

Phylogenetic reconstruction


Phylogeny reconstruction

Phylogenetic reconstruction

  • Rooted trees


Phylogeny reconstruction

Phylogenetic reconstruction

  • Rooted trees

    Outgroup:


Phylogeny reconstruction

Phylogenetic reconstruction

Introduction


Phylogeny reconstruction

Understanding Trees

Birds

Amphibians

Crocodiles

Birds

Mammals

Lizards

Snakes

Turtles

Crocodiles

Snakes

Lizards

Turtles

Mammals

Amphibians


Do these phylogenies agree

Do these phylogenies agree?

Figure 14.17


Phylogeny reconstruction

Branch lengths

A

B

C

D

A

B

C

D

1 nt change


Understanding trees

A

B

C

D

E

A

B

C

D

E

A

B

C

D

E

Understanding Trees

Trees can be used to describe taxonomic groups

Monophyletic

  • Paraphyletic

Polyphyletic


What is the relationship between taxonomic names and phylogenetic groups

Amniotes

Amphibians

Crocodiles

Mammals

Snakes

Lizards

Turtles

Birds

Amnion

What is the relationship between taxonomic names and phylogenetic groups?


What is the relationship between taxonomic names and phylogenetic groups1

Reptiles

Crocodiles

Snakes

Lizards

Turtles

Birds

Cold Blooded

What is the relationship between taxonomic names and phylogenetic groups?


What is the relationship between taxonomic names and phylogenetic groups2

Amphibians

Crocodiles

Rodents

Lizards

Snakes

Turtles

Birds

Bats

Wings

What is the relationship between taxonomic names and phylogenetic groups?


Polyphyletic example amentiferae

Polyphyletic example: Amentiferae


Polyphyletic example amentiferae1

Polyphyletic example: Amentiferae

Oaks

Walnuts

Willows

Evolution of catkins

Ancestor with separate flowers


Vertebrate phylogeny

Vertebrate Phylogeny

Are these groups monophyletic, paraphyletic or polyphyletic?

fish?

tetrapods? (= four limbed)

amphibians?

mammals?

ectotherms (= warm blooded)?


Constructing trees

Constructing Trees

Methods:

distance (UPGMA, Neighbor joining)

parsimony

maximum likelihood (Bayesian)


Distance methods phenetics

Distance Methods (phenetics)


Distance methods rely on clustering algorithms e g upgma

Distance methods rely on clustering algorithms (e.g. UPGMA)

D

B

A

Example 1: morphology

Trait 2

C

Distance matrix

Trait 1


Upgma

UPGMA

D

B

A

Example 1: morphology

Trait 2

C

Distance matrix

Trait 1

A

B


Upgma1

UPGMA

D

B

A

Example 1: morphology

Trait 2

C

Distance matrix

Trait 1

A

B

C

D


Distance methods with sequence data

Distance methods with sequence data

A: ATTGCAATCGG

B: ATTACGATCGG

C: GTTACAACCGG

D: CTCGTAGTCGA

Distance matrix

A

B


Distance methods with sequence data1

Distance methods with sequence data

New Distance matrix: take averages

A

B


Distance methods with sequence data2

Distance methods with sequence data

A

B

C

A

B

C

D


Distance methods with sequence data3

Distance methods with sequence data

A

B

C

A

B

C

D


Assumptions of distance methods

Assumptions of distance methods


Strengths and weaknesses of distance methods

Strengths and weaknesses of distance methods


Ii parsimony methods cladistics

II. Parsimony Methods (Cladistics)

Hennig (German entomologist) wrote in 1966

Translated into English in 1976: very influential


Applying parsimony

Applying parsimony

  • Consider four taxa (1-4) and four characters (A-D)

  • Ancestral state: abcd

Trait

Taxon


Applying parsimony1

Applying parsimony

  • Consider four taxa (1-4) and four characters (A-D)

  • Ancestral state: abcd

Unique changes

Convergences or reversals

  • 1234

  • a’bcda’b’c’d’a’b’c’da’b’cd

  • Trait

    b

    d’

    c’

    Taxon

    b’

    a’

    5 steps

    abcd


    Applying parsimony2

    Applying parsimony

    • Consider four taxa (1-4) and four characters (A-D)

    • Ancestral state: abcd

    Unique changes

    Convergences or reversals

    • 1432

    • a’bcda’b’cda’b’c’da’b’c’d’

    Trait

    d’

    c’

    Taxon

    b’

    a’

    4 steps

    abcd


    Strengths and weaknesses of parsimony

    Strengths and weaknesses of parsimony

    Strengths

    Weaknesses

    .


    Parsimony practice

    Parsimony practice

    Position

    Taxon1234567

    KAGTACCG

    LAAGACTA

    MAACCTTA

    NAAAGTTA

    Which unrooted tree is most parsimonious?

    N

    L

    L

    L

    K

    M

    2

    2

    K

    2

    M

    K

    N

    N

    M

    Plot each change on each tree. Positions 1 and 2 are done.

    Which positions help to determine relationships?


    Phylogeny reconstruction

    Inferring the direction of evolution

    ACGCTAGCTAGG

    Mouse

    Where did the mutation occur, and what was the change?

    Orangutan

    ACGCTAGCTAGG

    ACGCTAGCTAGG

    Gorilla

    ACGCTAGCTAGG

    Human

    ACGCTAGCTACG

    Bonobo

    ACGCTAGCTACG

    Chimp


    Iii maximum likelihood and bayesian

    III. Maximum likelihood (and Bayesian)


    Maximum likelihood a starting sketch

    Transitions

    Transversions

    A

    G

    T

    C

    Maximum likelihood: a starting sketch

    • Probabilities

      • transition: 0.2transversion: 0.1no change 0.7

    Find the tree with the highest probability


    Maximum likelihood a starting sketch1

    Transitions

    Transversions

    A

    G

    T

    C

    Maximum likelihood: a starting sketch

    • Probabilities

      • transition: 0.2transversion: 0.1no change 0.7

    P = (.7)(.1)(.2)(.7)(.7)

    Find the tree with the highest probability


    Maximum likelihood a starting sketch2

    Transitions

    Transversions

    A

    G

    T

    C

    Maximum likelihood: a starting sketch

    • Probabilities

      • transition: 0.2transversion: 0.1no change 0.7

    P = (.7)(.1)(.2)(.7)(.7)

    P = (.7)(.1)(.7)(.7)(.7)

    P = (.1)(.2)(.7)(.7)(.2)

    Find the tree with the highest probability


    Assessment of maximum likelihood also bayesian

    Assessment of Maximum Likelihood (also Bayesian)

    • Strengths

    • Weaknesses


    Characters to use in phylogeny

    Characters to use in phylogeny

    • Morphology

    • DNA sequence


    Challenges of using dna data

    Challenges of using DNA data

    Alignment can be very challenging!

    Taxon 1AATGCGC

    Taxon 2AATCGCT

    Taxon 1AATGCGC

    Taxon 2


    Informative sequences evolve at moderate rates

    Informative sequences evolve at moderate rates

    • Too slow?

      • not enough variation

      • Taxon 1AATGCGC

      • Taxon 2AATGCGC

      • Taxon 3AATGCGC

    Polytomy


    Example of insufficient evidence metazoan phylogeny

    Example of insufficient evidence: metazoan phylogeny

    Metazoans

    Fungi


    Challenges sunflower phylogeny

    Challenges: sunflower phylogeny

    • Recent radiation (200,000 years)

    • Many species, much hybridization

    • Need more rapidly evolving markers!!

    = 15 spp!

    = 12 spp!


    Informative sequences evolve at moderate rates1

    Informative sequences evolve at moderate rates

    • Too fast?

      • homoplasy likely

      • “saturation” – only 4 possible states for DNA

      • Taxon 1ATTCTGA

      • Taxon 2GTAGTGG

      • Taxon 3CGTGCTG

    Polytomy


    Saturation

    Saturation

    • Imagine changing one nucleotide every hour to a random nucleotide

    • Split the ancestral population in 2.

    ACTTGCT

    ACCTGAA

    AGCGGAA

    ACCAGAA

    ACGTGCT

    ACGAGCT

    GCGATCC

    GAGCTCC

    AGCCTCC

    8 hours

    12 hours

    One hour

    Four hours

    Red indicates multiple mutations at a site

    24 hours?


    Saturation mammalian mitochondrial dna

    Saturation: mammalian mitochondrial DNA


    Forces of evolution and phylogeny reconstruction

    Forces of evolution and phylogeny reconstruction

    How does each force affect the ability to reconstruct phylogeny?

    mutation?

    drift?

    selection?

    non-random mating?

    migration?


    Phylogeny case study i whales

    Phylogeny case study I: whales

    Are whales ungulates (hoofed mammals)? Figure 14.4


    Whales dna sequence data

    Whales: DNA sequence data

    Hillis, D. A. 1999.

    How reliable is this tree? Bootstrapping.


    How consistent are the data

    How consistent are the data?

    • Take the dataset (5 taxa, 10 characters)

    • Create a new data set by sampling characters at random, with replacement


    Phylogeny reconstruction

    Whales: DNA sequence data

    Hillis, D. A. 1999.


    Molecular clocks

    Molecular clocks


    Basic idea of molecular clocks

    Basic idea of molecular clocks

    chimps

    6 substitutions

    humans

    whales

    60 substitutions

    hippos

    56 mya


    Challenges for phylogeny gene flow

    Challenges for phylogeny: gene flow


    Sunflower annuals

    Sunflower annuals


    Different genes may have different histories

    Different genes may have different histories!


    Phylogeny summary

    Phylogeny summary


    Phylogeny study questions

    Phylogeny study questions

    • Explain in words the difference between monophyletic, paraphyletic, and polyphyletic taxa. Draw a hypothetical phylogeny representing each type. Give an actual example of a commonly recognized paraphyletic taxon in both animals and in plants.

      2) How can a reconstructed phylogeny be used to determine if a similar character in two taxa is due to homoplasy?

      3) Whales are classified as cetaceans, not artiodactyl ungulates. This makes artiodactyls paraphyletic – why? What is the evidence that whales belong in the artiodactyls?

    • Phenetics (distance methods) and cladistics (parsimony) differ in the ways they recognize and use similarities among taxa to form phylogenetic groupings. What types of similarity does each school recognize, and how useful is each type of similarity considered to be for identifying groups?


    Phylogeny study questions1

    Phylogeny study questions

    5) What is “bootstrapping” in the context of phylogenetic analysis, and why is this procedure performed?

    6) Why are maximum likelihood methods increasing in popularity for reconstructing phylogenies? In your answer, include a short description of how this method identifies the best phylogeny.

    7) For what kinds of data can maximum likelihood methods of phylogeny construction be used? Why is this so? What types of data are typically not used, and why?

    8) Would animal mitochondrial DNA provide a reasonable molecular tool for evaluating deep phylogenetic relationships between animal phyla? What about ribosomal DNA? Justify your answers.

    9) Integrative question: Draw a pair of axes with “Time since divergence” on the x axis and “percent of sites that are the same” on the y axis. Draw a graph that shows the basic pattern for third codon sites: is your graph linear? Explain why or why not.


    Phylogeny study questions2

    Phylogeny study questions

    10)You are studying a group of species that lives in two very different environments. You build two phylogenies: one is based on a locus that is probably under divergent selection in the two environments, while the other phylogeny is based on a neutral locus. Which phylogeny would be more likely to represent the species history? why?

    11) For a number of years, Anolis lizards are found in similar micro-habitats on many separate islands in the Carribean are very similar to each other (for example, large lizards that feed on the ground, smaller lizards that feed on tree trunks, and very small lizards that feed at the tops of branches). Two different, historical explanations have been proposed to explain this pattern: each morph has evolved repeatedly on each island, or each morph has evolved just once, then dipsersed. Sketch a phylogeny that would support each hypothesis.

    12) Integrative question: the Cameroon lake cichlid phylogeny, showing that the lake species were monophyletic, was based on mitochondrial DNA. Explain why this might not reflect the species history. How could you be more certain about the phylogeny?

    13) Explain why allopolyploid taxa pose problems for phylogenies.


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