Scott Baker and Stephen Palumbi (1994)

4.1 How to Read an Evolutionary Tree

• An evolutionary tree, also known as a phylogenetic tree or a phylogeny, is a diagram showing the history of divergence and evolutionary change leading from a single ancestral lineage to a suite of descendants.

How to Read Time on an Evolutionary Tree

Figure 4.1 Darwin’s evolutionary trees (a) An evolutionary tree Darwin sketched in his

Notebook B: Transmutation of Species (1987–1838). (b) A portion of the evolutionary tree that was the only illustration in On the Origin of Species (1859).

• Phylogenies, also known as evolutionary trees, are hypotheses about the history of descent with modification from a common ancestor that produced a set of species or other taxa.
• Time flows along a phylogeny from the root toward the branch tips.

How to Read Relationships on an Evolutionary Tree

• The evolutionary relationships among species on a phylogeny are defined by the relative time elapsed since they last shared common ancestors.

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• Lineages that share more recent common ancestors are considered more closely related.

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• Sister species: They are each other’s closest living relatives.

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• Evolutionary Trees Do Not Show Everything.

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• Evolutionary Trees Can Be Drawn in Various Styles.

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Evolutionary relationships are depicted solely by the order of branching in a phylogeny.�

Evolutionary Trees Are Hypotheses.�

4.2 The Logic of Inferring Evolutionary Trees

Phylogeny Inference in an Ideal Case

• In an ideal case, we can infer the evolutionary history of a set of species from their nested sets of shared evolutionary innovations.

Key Concepts in Phylogeny Inference

• An evolutionary novelty, or derived character, is known as an apomorphy (“separate form”).

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• Ancestral character, which is also known as a plesiomorphy (“near form”).

Key Concepts in Phylogeny Inference

• A derived character shared by two or more lineages, is called a synapomorphy (“similarly separate form”)

Figure 4.8 A character can be

a plesiomorphy in one context

and an apomorphy in another

Key Concepts in Phylogeny Inference

• A monophyletic group, also known as a clade, consists of an ancestor and all of its descendants.

Key Concepts in Phylogeny Inference

• A group consisting of an ancestor and some, but not all, of its descendants, is described as paraphyletic.

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• A group that contains some, but not all, of an ancestor’s descendants, and that also excludes the ancestor, is called polyphyletic.

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Figure 4.10 Major monophyletic groups of tetrapods

Gray triangles at branch tips represent diversifications

within monophyletic groups that could, space permitting,

be represented by multifarious evolutionary trees.

Polytomy

• Uncertainty about the order of branching in a phylogeny is indicated by polytomies—nodes where a lineage splits into more than two descendant lineages simultaneously.

Phylogeny Inference in Non-ideal Cases

Figure 4.11 Three imaginary

antelope species illustrate a

non-ideal case for phylogeny

inference

Outgroup Analysis

• Outgroup analysis involves including in our historical reconstruction one or more additional species (Maddison et al. 1984).

Figure 4.12 Outgroup analysis

Adding another species to

our reconstruction allows us to

make inferences about the most

recent common ancestor of the

ingroup.

Parsimony Analysis

• Under parsimony analysis, we prefer the hypothesis that requires the fewest evolutionary changes in the characters of interest (see Felsenstein 2004).

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• Most real examples do not work like our ideal case. Different characters often suggest different evolutionary relationships. In such circumstances, we consider all possible evolutionary trees as viable hypotheses and compare them using any of several criteria. One criterion is parsimony—the minimum amount of evolutionary change implied by a tree.

The Number of Possible Trees

• With four species in the ingroup, there are 15 possible bifurcating trees.
• With five species, there are 105. With 10 species, there are 34,459,425—more than the number of seconds in a year.
• It should be obvious why, in practice, most parsimony analyses are carried out with the assistance of computers.

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Convergence and Reversal

• The independent appearance in different lineages of similar derived characters is called convergent evolution.

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• The loss of derived traits in a lineage, resulting in a return to the ancestral condition, is called reversal.

Homoplasy

• Similarity in character states due to convergence and/or reversal is called homoplasy.
• Many of the complications in inferring phylogenies result from convergent evolution and reversal.
• The independent appearance of a character’s state in more than one place on a phylogeny is called homoplasy.

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Reversals complicate phylogeny inference

Reversals Complicate Phylogeny Inference

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How can we tell if the similar character is a convergence or a reversal ?

Close Relatives of Whales ?

Close Relatives of Whales ?

Sequence data for parsimony analysis

Genetic distances for cluster analysis

The presence of a SINE or LINE at loci 4-7 defines a clade of whales and hippos

The prokaryotes, dicotyledenous plants ("dicots"), and fish are all examples of paraphyletic groups.

Did chameleons speciate when Gondwanaland broke up?

This tree shows the relationships among chameleon groups predicted by the Gondwanaland breakup hypothesis

This tree shows the actual relationships among chameleons

Aphids and their bacterial endosymbionts

Aphids insert an organ called a stylet into plant vascular tissues and suck sap.

Specialized aphid cells are stained blue in this micrograph; the bacterial cells inside are stained green