Taxonimic evidence 3; Phylogenetic inference/ tree building

Tree terminology

dichotomy

a branch point where two lineages diverge from a common ancestor

polytomy

more than two lineages descend from a single ancestral lineage

pleisiomorphy

an ancestral character state or a trait that is present in the ancestor of a group and shared by some or all of its descendants

what is a monophyletic group?

a group includ8ing a common ancestor and all of its descendants

a clade

one “cut” from a phylogenetic tree

A group composed of an ancestor and all of its
descendants; diagnosed by synapomorphies, a
clade.

apomorphic

derived characters (not pleisiomorphic)

sympleisiomorphies

shared ancestral characters

not useful

root

common ancestor of whole group

synapomorphy

shared derived characters

topology

the shape of the tree (the connections between branches)

branches can be rotated at a node, w/out changing relationships among the taxa

paraphyletic group

a group containing a common ancestor and some, but not all, of its descendants; diagnosed by sympleisiomorphies

polyphyletic group

a group w/ 2 or more ancestors, but not including the true common ancestors of its members

ANA grade is an example of what group

paraphyletic

Phylogenetic inference

1. Obtaining information to develop phylogeny
-kinds of characters
2. Developing a phylogeny
-distinguishing synapomorphies
-rooting the tree with an outgroup
-optimality criteria for constructing trees
-parsimony vs. distance methods
3. Evaluating the phylogeny
-statistical support
-weaknesses of reconstruction methods
4. What do you do with a phylogeny?

developing a phylogeny

• distinguishing synapomorphies

• rooting the tree with an outgroup

• optimality criteria for constructing trees

• parsimony v. distance methods

phylogeny reconstruction

The most closely related taxa should share the
most traits (be most similar)
• Relies on the assumption that similarity is due
to shared common ancestry (homology)
• Specifically, relies on synapomorphies: shared
derived traits that characterize a
monophyletic group

must be distinguished from homoplasy: similarity that is not due to common ancestry

homoplasious traits are parallelisms or reversals: not homologous

what are 2 traits not useful in phylogeny reconstruction

• sympleisiomorphy: shared ancestral traits, that are not derived in the group you’re looking at

• autapomorphy: a trait that is derived w/in one lineage: not shared with anything else

How do we pick out synapomorphies?

• use an outgroup to root the tree

  • helps to figure out polarity: order of appearance of traits in evolutionary time

• assume traits shared between outgroup and ingroup are ancestral

criteria for an outgroup

• must assume that all ingroup members are more closely related to one another than the outgroup

• outgroup must be separated from ingroup lineage BEFORE the ingroup diversified

3 possible trees for observed character states

Methods of building trees

• parsimony (maximum parsimony)

• distance methods - mainly neighbor joining

• require an explicit model of evolution

  • Maximum likelihood

  • Bayesian inference

• parsimony is easiest to understand and is intuitively appealing

Phylogenetic inference- parsimony

• minimizing the number of evolutionary changes

• Occam’s razor: principle that states “the simplest explanation is most likely correct”

• parsimony asserts that the tree w/ the least # of evolutionary changes required is the “correct” tree

• the only informative characters in parsimony are synapomorphies

• no explicit model for evolution

What is the primary difference between a gene tree and a species tree?

A gene tree represents the phylogeny of a single gene, while a species tree represents the phylogeny of an entire species.

What is incomplete lineage sorting?

When gene trees do not reflect species trees due to shared ancestral variation not sorted properly during speciation.

Which of the following methods of tree construction minimizes the number of evolutionary changes?

Parsimony

In a phylogenetic tree, what does a monophyletic group consist of?

A group composed of a common ancestor and all of its descendants.

Explain the difference between a synapomorphy and a homoplasy.

A synapomorphy is a shared derived trait that is used to define a monophyletic group. It indicates a common ancestry. A homoplasy, on the other hand, is a trait shared by species due to parallel evolution or evolutionary reversals, not common ancestry

What is homoplasy, and how does it affect phylogenetic tree building?

Homoplasy refers to similarity in traits due to parallel evolution or reversals, rather than shared ancestry. It can mislead phylogenetic tree reconstruction because it creates the appearance of shared traits between unrelated species, leading to inaccurate tree relationships.