phylogeny reconstruction - g404.sitehost.iu.edu 15 - phylogenetic reconstruction.pdf2. determine the...

Department of Geological Sciences | Indiana University (c) 2011, P. David Polly

G404 Geobiology

(Polly, 2006)

Reading: Gregory, 2008. Understanding Evolutionary Trees

Trees, Methods and Characters

Phylogeny Reconstruction


G404 Geobiology

Lab tomorrow

Meet in Geology GY522

Bring computers if you have them (they will be more important next week and the week after)

Download and save PHYLIP program (no installation) (http://evolution.genetics.washington.edu/phylip.html)

Download and install Mesquite program suite (http://mesquiteproject.org/mesquite/mesquite.html)

http://evolution.genetics.washington.edu/phylip.html

http://evolution.genetics.washington.edu/phylip.html


G404 Geobiology

Key ingredients of phylogenetic analysis

❖ An understanding of the characteristics of a group of organisms

❖ A list of characters that vary among the group

❖ A tabulation of the state of the character in each member of the group

❖ Information on which state is ancestral for the group for each character

❖ A formatted data file that can be used with programs that perform phylogenetic analysis

❖ A computer and software that are capable of performing the analysis

❖ An understanding of phylogenetic trees to aid in interpreting the results


G404 Geobiology

Root

Branch(edge)

Internal node(hypotheticalancestor)

Terminal node(leaf, tip)

After Page & Holmes, 1998, Molecular Evolution: a Phylogenetic Approach

Tree terminology


G404 Geobiology

A B C D E

((A,B), (C, (D,E)))After Page & Holmes, 1998, Molecular

Evolution: a Phylogenetic Approach

Trees show closeness of relationshipTrees are read from bottom up, with each node representing an ancient speciation that lead to its descendant branches

Tree shows recency of common ancestry, same as showing nested sets

Sets can be drawn as a tree, or they can be written in parenthetical form

The parenthetical form is very close to the file format used by many programs to store or analyze trees

Examples: A and B are more closely related to one another than either is to C, D, or E.

C is more closely related to D and E than to A or B.

A and B share a more recent common ancestor than either does with C, D, or E.


G404 Geobiology

A B C D ABCD AB C D

= =

After Page & Holmes, 1998, Molecular Evolution: a Phylogenetic Approach

Cladograms are like mobilesCladograms are types of trees that show recency of common ancestry

Order of tree labels can vary without changing the meaning of the cladogram


G404 Geobiology

Baum, et al., 2005. The tree-thinking challenge. Science, 310; 979-980.

Tree-thinking challenge


G404 Geobiology

Different trees for different purposesSome differ simply by what is represented in the tree diagram

Some differ by the method used to construct them from data

After Page Holmes, 1998, Molecular Evolution: a Phylogenetic Approach

=

Cladogram: shows only recency of common ancestry

This axis means nothing

This

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hing

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Amou

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f cha

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Tim

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Additive Tree:shows recency of common ancestry

by branching pattern and evolution changeas branch lengths

Ultrametric Tree: shows recency of common ancestry

by branching pattern and time as branch lengths


G404 Geobiology

Didelphis

Dimetrodon

Tyrannosaurus

Didelphis

Dimetrodon

Tyrannosaurus

0 = absence of synapsid fenestra1 = presence of synapsid fenestra

0

0

1

01 1

Didelphis

Dimetrodon

Tyrannosaurus

01 1

0 1

11


Cladograms are constructed from character evolutionCharacter changes can be mapped onto trees using any one of several conventions


G404 Geobiology

Apomorphies PlesiomorphiesSynapomorphy

Autapomorphy Homoplasy

Terminology for characters on a treeCharacter states that evolve above the root (or a particular node) are “derived characters” or apomorphies

Character states present at the root are “ancestral characters”, “primitive characters”, or plesiomorphies

Synapomorphies are apomorphies shared by common ancestry (these character states are homologous and provide evidence of close relationship)

Autapomorphies are apomorphies found in only one tip (they are interesting, but don’t provide evidence of relationship)

Homoplasy is the evolution of a derived character independently on a tree so that it is shared by two tips, but not their common ancestor (same as “analogy”)



G404 Geobiology

Characters versus character statesA character is a feature that can be recognized, named, and described, such as a bone or a fenestra

A character state is the particular configuration of the character in a specific taxon

a character with states is called a “meristic character”, distinct from a “continuous character” or “quantitative character”, which is a character that is measured and can take on an infinite number of continuous values.

State A: quadratojugal present, large

State B: quadratojugal present, small

State C: quadratojugal

absent

Character: quadratojugal condition


G404 Geobiology

Methods for phylogeny reconstruction

Parsimony (=maximum parsimony, =cladistics). Uses only derived states of meristic characters to construct a tree based on “parsimony”. Parsimony is defined as minimizing the number of character states that evolve on the tree or, in other words, finding the shortest tree or finding the tree that makes the fewest assumptions of homoplasy.

Maximum likelihood (=ML). Uses derived states of meristic characters or quantitative characters to construct a tree based on the probabilities of character states changing on the tree. The probability of change is estimated from the data. ML trees are based on the probability that a particular model of character change and the observed character states would give rise to a particular tree. The tree with the highest probability, or likelihood, is the one favored.

Bayesian. Similar to maximum likelihood, but offers the possibility of easily combining different kinds of data (e.g., morphological and molecular) and offers the possibility of taking into account our confidence in relationships based on prior work.


G404 Geobiology

Recipe for a parsimony analysis

1. Observe and compare morphology to identify characters and character states. Best practice is to systematically work through the entire organism from nose to tail finding all characters that vary.

2. Determine the plesiomorphic and derived states of each character using one of several methods (outgroup method is the most accepted).

3. Score the characters and states in a data matrix, with one row for each character and one column for each taxon. Plesiomorphic state is given a 0, derived states a 1 (or an integer greater than one for a multistate character).

4. Use one of several software packages to find the shortest or most parsimonious tree from the data. These algorithms find the tree that maximizes the number of synapomorphies and minimizes the number of homoplasies.


G404 Geobiology

Methods for “polarizing characters”

Determining which states are plesiomorphic and which are apomorphic is known as “polarizing” a character. This step is essential for parsimony analysis.

Outgroup criterion. The preferred method. One or more outgroups are identified and the state common between them and the ingroup taxa is assumed to be the plesiomorphic states. Other states are left “unordered” or are given an order based on logic. Works well if the rate of character evolution is not high.

Paleontological criterion. The state that appears earliest in earth history is assumed to be plesiomorphic based on the logic that it evolved first. Works well if the fossil record is good.

Ontogenetic criterion. The state that appears first in embryonic development is assumed to be plesiomorphic based on the logic that the most general developmental state is likely to have evolved first. Dubious at best.

Commonality criterion. The state found in most taxa is assumed to be plesiomorphic based on the logic that among many taxa, some are likely to be outgroups. Works only in cases where the sample of taxa includes more outgroups than ingroups


G404 Geobiology

Protogyrinus

DiadectesCaptorhinus

Youngina

Kuhneosaurus

EdmontosaurusArchaeopteryx

Titanophoneus Dimetrodon

Amniota

The outgroup criterion at work

Outgroup state: large tabular, postparietal, supratemporal, infratemporal

Ingroup states: small or absent tabular, postparietal, supratemporal, infratemporal, often positioned on posterior of cranium

Non-amniotes Amniotes

Character 1: postparietal condition. 0 - present and large; 1 - small or absent.

Character 2: tabular condition. 0 - present and large; 1 - small or absent.

Character 3: supratemporal condition. 0 - present and large; 1 - small or absent.

Character 4: infratemporal condition. 0 - present and large; 1 - small or absent.


G404 Geobiology

Cladogram based on posterior skull bones

Captorhinus

Archaeopteryx

Dimetrodon

Youngina

Kuhneosaurus

Edmontosaurus

Diadectes

Protogyrinus

Character matrix Consensus cladogram950 equally parsimonious trees foundTree length: 4CI: 1.0


G404 Geobiology

Tree support

Capt

orhi

nus

Arch

aeop

tery

x

Dim

etro

don

Youn

gina

Kuhn

eosa

urus

Edm

onto

saur

us

Dia

dect

es

Prot

ogyr

inus

0 1Character 1:0 1Character 2:0 1Character 3:0 1Character 4:

Cladogram (consensus)950 equally parsimonious trees foundTree length: 4CI: 1.0

The support for a tree varies according to the ability of the data to unambiguously resolve nodes

The simplest index of tree support in parsimony is the consistency index

Calculated as the number of changes on the tree (tree length) divided by minimum number of changes in data (number of character states in all characters)

Here there are four characters each with one derived state, so minimum number of changes is 4.0

There are 4 changes on tree, so consistency index is 1.0


G404 Geobiology

Star tree Partially resolved Fully resolved(fully bifercating)

Polytomy

Character data are not always able to fully resolve relationshipsTotally unresolved tree is a “star tree”

“Hard polytomies” result from data support

“Soft polytomies” are when data are contradictory about relationships



G404 Geobiology

Scientific papers for further readingBaldauf, S. L. 2003. Phylogeny for the faint of heart: a tutorial. TRENDS in Genetics, 19: 345-351.

de Queiroz, K. and J. A. Gauthier, 1992. Phylogenetic taxonomy. Annual Reviews of Ecology and Systematics, 23: 449-480.

Gauthier, J., A. G. Kluge, and T. Rowe. 1988. Amniote phylogeny and the importance of fossils. Cladistics, 4: 105-209.

Gregory, T. R. 2008. Understanding Evolutionary Trees. Evolution Education Outreach, 1: 121-137. [Required reading]

Padian, K., D.R. Lindberg, and P.D. Polly, 1994. Cladistics and the fossil record: the uses of history. Annual Reviews of Earth and Planetary Sciences, 22: 63-91.

phylogeny reconstruction - g404.sitehost.iu.edu 15 - phylogenetic reconstruction.pdf2. determine the...

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