what is phylogeny? the evolutionary history of a group. –families, genera, species, genes...

What Is Phylogeny?

• The evolutionary history of a group.– Families, genera, species, genes

• Phylogeny is not knowable (in most cases).

• Many methods exist to estimate phylogeny.

Phylogenetic relationships• Two lineages are more closely related to each other than to

some other lineage if they share a more recent common ancestor.

• Phylogenetic hypotheses are hypotheses of common ancestry

Phylogenetic Trees

A B C D E F G H I J

ROOT

polytomy

terminal branches

interiorbranches

node 1 node 2

LEAVES

A CLADOGRAM

CLADOGRAMS AND PHYLOGRAMS

ABSOLUTE TIME or DIVERGENCE

RELATIVE TIME

A B

C DE

FG

HI

J

A B C D E F GH I J

Trees - Rooted and Unrooted

ROOTA

B

C

D E

F

GH

I

J

A B C D E F GH I J

ROOT

A B C D E F G H I J

ROOT

Systematics: The study of the classification of the immense diversity of life

Phylogenetic Systematics: The use of phylogenetic methodology to resolve

monophyletic groups

http://tolweb.org/tree/phylogeny.html

Tree of Life

Reconstructing Evolutionary Trees

Phylogeny: Evolutionary history of a group.

Phylogenetic Tree: Shows evolutionary history graphically.

A phylogeny must be inferred from datathat are likely to reveal evolutionary history

Similar structures or behaviors in different organisms, which are supposed to represent modifications of a single evolutionary

novelty in a common ancestor

Homology

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Similar function, but not homologous

Different function, but homologous

Similar structures or behaviors in different organisms, which are supposed to represent modifications of a single evolutionary

novelty in a common ancestor

Homology

Synapomorphies

Homologous traits or states that are shared among species because they share a common ancestor

Synapomorphy

Cladistics

Methods of phylogeny reconstruction where monophyleticgroups are identified on the basis of shared derived characters.

Homoplasy

Shared derived similarities, that are not based on a singular common origin (= homology), but on an independent origin in

different taxa.

Convergence: Shared derived similarities, that are not based on a singular common origin (= homology ), but on an independent origin

in different taxa.

Types of Homoplasy

Reversal :The secondary presence of an apparently "primitive” character state,

Example: Wings in insects, birds, and bats

Example: Aquatic mode of life for fish, terrestriality for tetrapods, reversal to aquatic life in whales

Homoplasy - independent evolution

HumanLizard

Frog Dog

TAIL (adult)

absentpresent

• Loss of tails evolved independently in humans and frogs - there are two steps on the true tree

Homoplasy: Misleading evidence of phylogeny

• If misinterpreted as a synapomorphy, the absence of tails would be evidence for a wrong tree: grouping humans with frogs and lizards with dogs

Human

Frog

Lizard

Dog

TAIL

absentpresent

Homoplasy: Reversal

• Reversals are evolutionary changes back to an ancestral condition

• As with any homoplasy, reversals can provide misleading evidence of relationships

True tree Wrong tree101 2 3 4 5 67 8 91 2 3 4 5 6 7 8 9 10

• How do we sort out phylogeny from a mixture of signal (synapomorphies) and noise (homoplasy).

• Cladistic methodology utilizes the principle of parsimony.

• Parsimony= The tree that requires the fewest number of evolutionary steps to explain the data is preferred.

So how do we construct trees with a sample of homologous characters?

Tree Reconstruction with Parsimony


Tree 1 Tree 2 Tree 3

Mutation=Evolutionary Step


Tree 1 Tree 2 Tree 3

Character 2

I(A)

II(G)

III(A)

IV(G)

I(A) II(G)

III(A) IV(G)

I(A) II(G)

III(A)IV(G)

I(A)

II(G)

III(A)

IV(G)

or orI(A) II(G)

III(A)IV(G)

What to do when some characters tell you one thing and others tell you something else

(Homoplasy)?

The most parsimonious pattern of character change is noted for each character separately, for each tree.

The number of changes is summed across charactersfor each tree.

The preferred tree is the one that implies the fewest overall character changes.

Parsimony with Multiple Characters

1

2

3

Tree 1 is favored under the criterion of Parsimony

How to search all possible trees?

• The number of possible trees increases exponentially with the number of species making exhaustive searches impractical for many data sets

• But we have a larger data set to consider, so using parsimony methodology, we need to utilize a way to search for the best tree without evaluating all possible trees.

Finding optimal trees: Heuristic searches

• Heuristic methods are used to search tree space for most parsimonious trees by building or selecting an initial tree and swapping branches to search for better ones

• The trees found are not guaranteed to be the most parsimonious-they are best guesses

Finding optimal trees: Heuristics

• Tree bisection and reconnection (TBR)

Parsimony: Advantages

• Simple method - easily understood operation• Does not seem to depend on an explicit model of

evolution• Should give reliable results if the data is well structured

and homoplasy is either rare or widely (randomly) distributed on the tree

what is phylogeny? the evolutionary history of a group. –families, genera, species, genes...

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