phylogenetic analysis – part 2
DESCRIPTION
Phylogenetic Analysis – Part 2. Spring 2013. Outline. Why do we do phylogenetics (cladistics)? How do we build a tree? Do we believe the tree? Applications of phylogenetics (cladistics). Why do we do phylogenetic analyses?. Evolutionary interpretation of relationships between organisms. - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/1.jpg)
Phylogenetic Analysis – Part 2
Spring 2013
![Page 2: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/2.jpg)
Outline Why do we do phylogenetics
(cladistics)?
How do we build a tree?
Do we believe the tree?
Applications of phylogenetics (cladistics)
![Page 3: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/3.jpg)
Why do we do phylogenetic analyses?
Evolutionary interpretation of relationships between organisms.
More reliable method of ascertaining the best hypothesis for how the organisms diverged from common ancestors.
Provides a better rationale for circumscribing taxonomic groups.
Enables testing of multiple hypotheses of relationships and character evolution based on specific character transformations.
![Page 4: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/4.jpg)
Willi Hennig(1913-1976)
German Entomologist (Diptera)
![Page 5: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/5.jpg)
Warren Herbert Wagner(1920-2000)
American Botanist (Pteridophytes,
Dendrogramaceae)
![Page 6: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/6.jpg)
How do we build a tree? Data: Types of characters
Look for synapomorphies
Assemble the hierarchy of synapomorphies according to the principle of parsimony
![Page 7: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/7.jpg)
Parsimony The idea that the simplest hypothesis is the
best explanation given the assumptions of the analysis.
Also known as Occam’s Razor In systematics, we look for the shortest trees
in any given phylogenetic analysis (maximum parsimony)…
…even though we know that evolution doesn’t necessarily proceed in a parsimonious manner.
![Page 8: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/8.jpg)
Data: type of charactersCharacter Selection:
Must study each individual character to assure comparisons of homologous characters, and interpretation of the direction of character state transformations.
Some sources of characters: 1) morphology (external structure) or anatomy (internal
structure)
2) biochemical (photosynthetic pathway, pigmentation pathways, etc.)
3) chromosome numbers
4) nucleotide sequence data ( a t c g )
![Page 9: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/9.jpg)
Character states Presence vs. absence (0 or 1): always binary
(two states) Other binary characters (0 or 1): yellow vs.
white flowers; range of measurements (quantitative)
Multi-state characters (3 or more states): e.g., yellow, white, or pink flowers or a t g c for nucleotide sequence data
For binary or multi-state characters, can hypothesize the direction of evolutionary change (transformation series)
![Page 10: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/10.jpg)
Fig. 2.2
Pollen wall thickness µm (x axis)
![Page 11: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/11.jpg)
Fig. 2.4 Examples of character state transformations
![Page 12: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/12.jpg)
But how to hypothesize direction?
We usually have some working knowledge of the group under study (ingroup).
We choose a group thought to be closely related to the ingroup to serve as the outgroup as a basis of comparison.
Character states in the outgroup are assumed to be ancestral (plesiomorphic).
This allows us to establish the direction of character state transformation.
![Page 13: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/13.jpg)
Phylogenetics or Cladistics
Bachia
Bachia
![Page 14: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/14.jpg)
We need an outgroup, so wechoose the closely related genus Attigalea (there isevidence for this from otherstudies).
Cladistics
Attigalea
Bachia
Ingroup
![Page 15: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/15.jpg)
Cladistics: characters
1. Leaf arrangement: alternate (0) or opposite (1)
2. Leaf midrib: white (0) or green (1)3. Leaf apex: rounded (0) or spiny (1)4. Sepals: present (0) or absent (1)5. Flower color: yellow (0) or blue (1)6. Subtending floral bracts: absent (0) or
present (1)
![Page 16: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/16.jpg)
Cladistics: characters
1. Leaf arrangement: alternate (0) or opposite (1)
2. Leaf midrib: white (0) or green (1)3. Leaf apex: rounded (0) or spiny (1)4. Sepals: present (0) or absent (1)5. Flower color: yellow (0) or blue (1)6. Subtending floral bracts: absent (0) or
present (1)
![Page 17: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/17.jpg)
Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0
Outgroup (Attigalea) Ingroup (Bachia)
![Page 18: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/18.jpg)
Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0
![Page 19: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/19.jpg)
Cladistics7 8 2 4 3 5 6 1
Leaves opposite
Sepals absent
![Page 20: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/20.jpg)
Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0
![Page 21: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/21.jpg)
Cladistics7 8 2 4 3 5 6 1
Leaves opposite
Sepals absent
Midrib green
![Page 22: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/22.jpg)
Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0
![Page 23: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/23.jpg)
Cladistics7 8 2 5 3 4 6 1
Leaves opposite
Sepals absent
Midrib green
Blue flowersFloral bractspresent
![Page 24: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/24.jpg)
Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0
Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0
![Page 25: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/25.jpg)
purple fringe
sepals absent
floral bractspresent
midrib green
Length = 5 steps
Attigalea Bachia
![Page 26: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/26.jpg)
Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0
Homoplasy?Polymorphism in the outgroup
![Page 27: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/27.jpg)
purple fringe
sepals absent
floral bractspresent
midrib green
spiny leaftip
spiny leaf tip
Length = 7 steps
Attigalea Bachia
![Page 28: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/28.jpg)
Do we believe the tree? Various programs to generate trees. Various measures of statistical support
for the clades and for the characters. Can quantify the effects of homoplasy. Can test alternate arrangements to
examine the number of steps involved.
![Page 29: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/29.jpg)
purple fringe
sepals absent
floral bractspresent
midrib green
spiny leaftip
spiny leaf tip
Length = 10 steps (7 - 1 + 4)
Attigalea Bachia
![Page 30: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/30.jpg)
Phylogenetic Methodology1. Selection of taxa to study - Individuals, populations,
species, etc. identified as the units of comparison. One or more related groups (outgroups) necessary to “root” the trees.
2. The units under study described for as many characters as possible for which homology can be demonstrated or reasonably assumed. Character states assigned based on variation among the taxa in the ingroup and outgroup(s) and a priori hypotheses of the evolutionary direction of changes undergone by the character (character state polarization) are generated based on outgroup comparison.
3. A data matrix is assembled by scoring all taxa for all characters (ideally).
![Page 31: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/31.jpg)
Phylogenetic Methodology(continued)
4. Using various analytical principles (maximum parsimony), a cladogram is constructed using synapomorphic character state changes to determine the tree topology. Systematists are seeking to define monophyletic groups (= clades).
5. Evaluation of the statistical confidence in how robustly the data support the grouping of organisms into clades is done next.
6. The subsequent grouping and ranking of the organisms in the resulting clades is then applied to classification systems or other questions.
![Page 32: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/32.jpg)
Applications of phylogenetics
Classification
Biogeography
Many other possibilities (e.g., disease tracking, gene annotation)
![Page 33: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/33.jpg)
Cladistics and Classification- Classifications based on tree topologies…Is it the best
tree? Will new data and new tree topologies necessitate complete overhaul of classification?
- Remember, systematists would like to define and name monophyletic groups (clades). Is this always possible? Must we accept paraphyletic groups?
- Classifications must also be useful for communication. Do the groups truly represent the best evolutionary hypothesis, and yet are the classifications useful?
![Page 34: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/34.jpg)
Phylogenetics and Classification
![Page 35: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/35.jpg)
Phylogenetics and Classification
Fig. 2.19A-C
![Page 36: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/36.jpg)
Adansonia(baobab tree)
(Judd et al. 2008)
Phylogenetics and Biogeography
![Page 37: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/37.jpg)
Fig. 2.22
Phylogenetics andCharacter Evolution
![Page 38: Phylogenetic Analysis – Part 2](https://reader031.vdocuments.net/reader031/viewer/2022020208/56815fd3550346895dced430/html5/thumbnails/38.jpg)
Fig. 19.11
Phylogenetics and ConservationAnomochloa
bamboo bluegrassBig bluestem
Northern sea oats
Grama grass