Transcript BIO2093_DMS1_phylogeny

Phylogeny I
BIO2093 – Phylogenetics
Darren Soanes
Phylogenetics
• The study of evolutionary relationships
among groups of organisms.
• Phylogenetic tree: a hypothesis of the
order in which evolutionary events are
assumed to have occurred.
Phylogenetic tree
Parts of a tree
plural of taxon = taxa
Phylogenetic tree: evolutionary family tree
Nodes in the tree represent speciation
events, where an ancestral lineage gives
rise to daughter lineages.
Relationships in trees
Rooting a tree
outgroup
Root - most recent
common ancestor of
all the taxa in a tree
outgroup — a taxon outside the group of interest. All the members
of the group of interest are more closely related to each other than
they are to the outgroup. Used to root the tree.
Outgroup
Rooted and unrooted trees
rooted tree
unrooted tree
Types of trees
• A cladogram is a phylogenetic tree
formed using cladistic methods. It shows
branching pattern only.
• A phylogram is a phylogenetic tree that
has branch lengths proportional to the
amount of character change.
• A chronogram is a phylogenetic tree that
explicitly represents evolutionary time
through its branch lengths.
Cladistics
Classification into clades
based on shared derived
characters
(synapomorphies).
A synapomorphy is a
trait shared among
species because the
common ancestor of
those species also had
the trait.
Analogy
Homoplasy:
homoplastic character
state is a trait that is
shared by two or more
taxa because of
convergence,
parallelism or reversal
e.g modified nostrils
on top of head in
cetaceans and
dinosaur group
Macronaria.
Convergent evolution
Plant kingdom
Clades
A clade consists of an ancestor
organism and all its
descendants.
Clade = monophyletic group
Each monophyletic group can
be identified by one or more
synapomorphies.
Phylogenetic classification system
Phylogenetic groups are
based on clades
(monophyletic groups)
Phylogenetic classification system
Reptile is not a legitimate
phylogenetic grouping (unless
we include birds as reptiles) –
paraphyletic group
Birds are part of the clade
Dinosauria.
Phylogenetic classification system
Mono, poly and paraphyly
Polyphyletic group – ‘warm blooded’
Types of trees
• A cladogram is a phylogenetic tree
formed using cladistic methods. It shows
branching pattern only.
• A phylogram is a phylogenetic tree that
has branch lengths proportional to the
amount of character change.
• A chronogram is a phylogenetic tree that
explicitly represents evolutionary time
through its branch lengths.
Phylogram
Cladogram
Phylogram
Types of trees
• A cladogram is a phylogenetic tree
formed using cladistic methods. It shows
branching pattern only.
• A phylogram is a phylogenetic tree that
has branch lengths proportional to the
amount of character change.
• A chronogram is a phylogenetic tree that
explicitly represents evolutionary time
through its branch lengths.
Chronogram
Phylogram calibrated based
on fossil record
Constructing phylogenetic trees
Constructing phylogenetic trees
From studying fossils and lineages closely
related to the vertebrate clade, we
hypothesise that the ancestor of vertebrates
had none of these features
Constructing phylogenetic trees
Constructing phylogenetic trees
Parsimony
All other things being equal, the best hypothesis is the one
that requires the fewest evolutionary changes
Reading
• Freeman and Herron – Evolutionary
Analysis (4th Edition): Chapter 4
(Estimating Evolutionary Trees).
Summary
• Phylogenetic tree: a hypothesis of the
order in which evolutionary events are
assumed to have occurred.
• Constructed using shared derived
characters (synapomorphies).
• Parsimony: All other things being equal,
the best hypothesis is the one that
requires the fewest evolutionary changes.