Phylogeny Reconstruction

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1 Phylogeny Reconstruction Trees, Methods and Characters Reading: Gregory, Understanding Evolutionary Trees (Polly, 2006)

2 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) ( Download and install Mesquite program suite (

3 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

4 Tree terminology Terminal node (leaf, tip) Root Branch (edge) Internal node (hypothetical ancestor) After Page & Holmes, 1998, Molecular Evolution: a Phylogenetic Approach

5 Trees show closeness of relationship Trees 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 B C D E A and B share a more recent common ancestor than either does with C, D, or E. ((A,B), (C, (D,E))) After Page & Holmes, 1998, Molecular Evolution: a Phylogenetic Approach

6 Cladograms are like mobiles Cladograms are types of trees that show recency of common ancestry Order of tree labels can vary without changing the meaning of the cladogram A B C D D C B A B C D A = = After Page & Holmes, 1998, Molecular Evolution: a Phylogenetic Approach

7 Tree-thinking challenge Baum, et al., The tree-thinking challenge. Science, 310;

8 Different trees for different purposes Some differ simply by what is represented in the tree diagram Some differ by the method used to construct them from data This axis means nothing Cladogram: shows only recency of common ancestry = This axis means nothing Amount of change Additive Tree: shows recency of common ancestry by branching pattern and evolution change as branch lengths This axis means nothing Time Ultrametric Tree: shows recency of common ancestry by branching pattern and time as branch lengths This axis means nothing After Page Holmes, 1998, Molecular Evolution: a Phylogenetic Approach

9 Cladograms are constructed from character evolution Character changes can be mapped onto trees using any one of several conventions Didelphis Dimetrodon Tyrannosaurus Didelphis Dimetrodon Tyrannosaurus Didelphis Dimetrodon Tyrannosaurus = absence of synapsid fenestra 1 = presence of synapsid fenestra After Page Holmes, 1998, Molecular Evolution: a Phylogenetic Approach

10 Terminology for characters on a tree Character 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 Apomorphies Plesiomorphies Synapomorphy 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 ) Autapomorphy Homoplasy After Page Holmes, 1998, Molecular Evolution: a Phylogenetic Approach

11 Characters versus character states A 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. Character: quadratojugal condition State A: quadratojugal present, large State B: quadratojugal present, small State C: quadratojugal absent

12 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.

13 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.

14 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

15 The outgroup criterion at work Edmontosaurus Archaeopteryx Kuhneosaurus 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. Protogyrinus Diadectes Titanophoneus Dimetrodon Youngina Captorhinus Amniota Non-amniotes Amniotes Outgroup state: large tabular, postparietal, supratemporal, infratemporal Ingroup states: small or absent tabular, postparietal, supratemporal, infratemporal, often positioned on posterior of cranium

16 Cladogram based on posterior skull bones Captorhinus Archaeopteryx Dimetrodon Youngina Kuhneosaurus Edmontosaurus Diadectes Protogyrinus Character matrix Consensus cladogram 950 equally parsimonious trees found Tree length: 4 CI: 1.0

17 Tree support 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 Captorhinus Archaeopteryx Dimetrodon Youngina Kuhneosaurus Edmontosaurus Diadectes Protogyrinus 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 Character 1: 0 1 Character 2: 0 1 Character 3: 0 1 Character 4: 0 1 Cladogram (consensus) 950 equally parsimonious trees found Tree length: 4 CI: 1.0

18 Character data are not always able to fully resolve relationships Totally unresolved tree is a star tree Hard polytomies result from data support Soft polytomies are when data are contradictory about relationships Star tree Partially resolved Fully resolved (fully bifercating) Polytomy After Page Holmes, 1998, Molecular Evolution: a Phylogenetic Approach

19 Scientific papers for further reading Baldauf, S. L Phylogeny for the faint of heart: a tutorial. TRENDS in Genetics, 19: de Queiroz, K. and J. A. Gauthier, Phylogenetic taxonomy. Annual Reviews of Ecology and Systematics, 23: Gauthier, J., A. G. Kluge, and T. Rowe Amniote phylogeny and the importance of fossils. Cladistics, 4: Gregory, T. R Understanding Evolutionary Trees. Evolution Education Outreach, 1: [Required reading] Padian, K., D.R. Lindberg, and P.D. Polly, Cladistics and the fossil record: the uses of history. Annual Reviews of Earth and Planetary Sciences, 22:

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