Transcript Phylogeny

Phylogeny
Evolutionary history of a group of
organisms
• Phylogenetic tree: ancestor-descendant
relationships among populations/species
=Outgroup
Root
Branch
Node
Tip
Each phylogenetic tree is a hypothesis
• Approaches
– Phenetic – overall similarities between
populations (genetic distance – summarizes
average percentage of bases in a DNA sequence
that differ) More divergent populations are on
more distant branches
– Cladistic: based on shared derived characters
(synapomorphies)
• Synapomorphy: a trait that exists in a certain
group of organisms but exists in no others (due to
common ancestry)
• Monophyletic group: an ancestral species and ALL
of its descendants (based on synapomorphy)
• AKA: lineage, clade
• ONE Snip test: if you cut a branch and all the
branches and tips fall off, then it is monophyletic
5 of the 6 trees listed describe the same relationship. Which tree
is different?
• Homology (same source): derived from a
common ancestor
• Homoplasy (same form): similar but not due
to common ancestry.
Homologous (1) or Homoplasy (2)
a. the dorsal fins of a dolphin (mammal) and a
salmon (fish)
b. the flippers of a dolphin and arm of a human
c. a rhesus monkey’s tail and a human’s coccyx
d. the bracts (red leaves) of a poinsettia and green
leaves of a rose
e. the bracts (red leaves) of a poinsettia and red
petals of a rose
f. the scales on a reptile and the feathers on a bird
Basics of Phylogeny: Cladograms
Why don’t we place homologous characteristics on a tree twice?
This implies the characteristic evolved more than once
Recall this involves a random mutation (rare event) that
happens to occur in an organism that is in an environment
where this mutation creates a favorable adaptation.
This kind of thing takes millions of years (ex. limbs evolving
on fish). Very low probability it would happen more than
once:
But if this does happen, it is called convergent evolution
Place analogous characteristics on trees, but don’t CREATE
trees using them. (Fig 27.2 )
Using the basics of phylogeny
to construct the Tree of Life
Organism Classification: Before the Tree of Life
I. Linneaus
Organisms that didn’t move, made their own food: Plants.
Organisms that moved, ate others for food: Animals.
Problems with this system?
Organism Classification: Before the Tree of Life
II. Then…fundamental division at the cellular level
between prokaryotes and eukaryotes discovered
Eukaryote: “true-kernel”
Prokaryote: “before-kernel”
~__Nucleus (membrane bound)___ ~_no nucleus__
~__larger______________
~__smaller_____________
Organism Classification: Before the Tree of Life
III. 1960s = 5 kingdoms
prokaryotes
Set of shared characteristics defined
kingdom members.
eukaryotes
Most Characteristics:
•_______morphological________
Major Changes in Organism Classification:
The Tree of Life
Carl Woese et al: __RNA_____to study relationships
Compared gene sequence for ____16S and 18 S RNA___________
•in all cells
•make up part of ribosomes
•location of protein synthesis
Eukaryote
ribosomes
Prokaryote
Why compare sequence for rRNA gene?
Ribosomes found in ALL organisms and serve
the same function
Ribsosomal RNA (rRNA) therefore in ALL organisms
The DNA that encodes for rRNA in ALL organisms
This gene happens to be HIGHLY conserved (similar)
among species but not identical
The amount of change in the DNA sequence of this gene
over time is consistent and understood
So what happens when organisms are
classified this way?
Major division among organisms NOT between prokaryotes
and eukaryotes but between Bacteria, Archaea, Eukarya
I. Bacteria
II. Archaea
III. Eukarya
Prokaryotes
~no memb-bound organelles
(no nucleus,mitochondria, etc.)
~circular chromosomes
~single-celled
Eukaryotes
~memb-bound organelles
~linear chromosomes
So what happens when organisms are
classified this way?
BUT, Molecular Data conflicts with morphological data…
I. Bacteria
II. Archaea
Prokaryotes
~no nucleus,
mitochondria, etc.
~circular chromosomes
~single-celled
III. Eukarya
Molecularly Similar
~rRNA sequence
~RNA polymerase
~How DNA is
packaged in the cell
FYI: You should be able to
Draw both types of trees
Place characteristics on trees in correct location
Be able to recall specific characteristics that create one
tree versus the other (ex. circular vs linear chromosomes and
complex versus simple RNA polymerase) so if a tree was
drawn for you, you could come up with the correct
characteristics
to place on a specific tree
Understand how work of Woese et al changed how we
classify organisms
Which of the following is more closely related
to green algae?
1. Red algae because they share the MRCA
2. Land plants because they share the MRCA
3. Red algae because it is also an algae
4. Land plants because they also have
chlorophyll (green)
Which of the following is more closely related
to land plants?
1. Chordates b/c they share the MRCA at the
root of the tree
2. Mollusks b/c they share the MRCA at the
root of the tree
3. Land plants are equally related to
Chordates and Mollusks b/c they share the
MRCA at the root of the tree
4. Neither b/c they don’t share a MRCA
Jellyfish are more closely related to chordates
than to fungi?
1. True because the MRCA of jellyfish and
chordates is above the MRCA of jellyfish
and fungi
2. True because the MRCA of jellyfish and
chordates is below the MRCA of jellyfish
and fungi
3. False because the MRCA of jellyfish and
chordates is above the MRCA of jellyfish
and fungi
4. False because jellyfish are equally as
related to chordates and fungi based on
their equal MRCA
Identify the tree that shows a different set of relationships between the
9 taxa than the other two trees.
1. The difference is in tree 1
2. The difference is in tree 2
3. The difference is in tree 3
If species a–i are a group of flowering plants, assume taxa a–d have red flowers,
taxa f–i have blue flowers, and taxa e has white flowers. Draw the locations of
flower color changes on trees 1–3. How are the three trees similar? How are they
different?
How do we know about the “history”
in the phylogenies?
• Fossil record is the only DIRECT evidence
• Fossil record is biased though
– Habitat bias
– Taxonomic bias
– Tissue bias
– Temporal bias
– Abundance bias
How do we get the “branches” on our
phylogenetic trees?
• Evolution.
• Sometimes there is fast and huge divergence
from a single ancestor
• =Adaptive radiation
• Why?
– Ecological opportunity
– Morphological innovation
Why don’t we see ALL the species that
ever evolved?
• Extinction
• Background rates
– Normal environmental change
– Emerging disease
– competition
• Mass extinction (above background average)
– Sudden, extraordinary environmental change