Transcript most recent common ancestor

Welcome to BIO 94!
TA: Jen
Email: [email protected]
Office hours:
Friday, 2:00-3:00, BS3 2130
Tree-thinking Quiz
BIO94 W16
Answers included
Quiz based on “The Tree-Thinking Challenge”, David A. Baum,* Stacey DeWitt
Smith, Samuel S. Donovan, Science 310, 979 (2005)
First, some terminology . . .
Terms associated with phylogenetic trees
Tips represent
terminal taxa (or
genes) of a lineage,
usually extant
(a.k.a. leaf, or
terminal node or
just a terminal)
A
B
C
D
E
Terms associated with phylogenetic trees
Nodes represent
branching or
splitting points on
a tree; may
represent extinct
or hypothetical
ancestor(s)
A
B
C
D
E
Terms associated with phylogenetic trees
B
C
D
Note: some trees have no ‘root’, to be discussed later
E
Time
“Root” refers to
the node at the
‘base’ of the tree;
represents the
common ancestor
of all descendant
taxa in the tree.
A
Terms associated with phylogenetic trees
Branches are the
parts of a tree
that connect the
node or the nodes
to the tips (aka
internodes, edges)
A
B
C
D
E
a
b
c
Note: branches such as a, b, and c are sometimes referred to as ‘internal branches’
Terms associated with phylogenetic trees
Topology of a tree
refers to the
overall pattern of
connectedness of
the nodes and
termimal taxa
A
B
C
D
E
Tree equivalence:
Format doesn’t matter, but attachment points do.
Pay attention to the branching pattern and nestedness (what
stacks within what).
None of this changes the relationships of the
taxa shown.
Tree equivalence:
Format doesn’t matter, but attachment points do.
Pay attention to the branching pattern and nestedness (what
stacks within what).
Is the frog more closely related to
the fish or the human?
Is the frog more closely related to
the fish or the human?
Consider the following evolutionary tree
or phylogeny . . .
fungus
green
algae
moss
fern
conifer
x
y
1. Referring to the tree above, which is an accurate statement of
relationships?
a) a moss is more closely related to a green alga than to a fern
b) a moss is more closely related to a fern than to a green alga
c) a moss is equally related to a green alga and a fern
d) a moss is related to a green alga but is not related to a fern
Consider another example . . .
fish
lizard
crocodile dinosaur
bird
x
y
2a. Referring to the tree above, which is an accurate statement of
relationships?
a) a crocodile is more closely related to a lizard than to a bird
b) a crocodile is more closely related to a bird than to a lizard
c) a crocodile is equally related to a bird and a fish
d) a crocodile is related to a lizard but is not related to a bird
Does this help?
2b. Referring to the tree above, which is an accurate statement of
relationships?
a) a crocodile is more closely related to a lizard than to a bird
b) a crocodile is more closely related to a bird than to a lizard
c) a crocodile is equally related to a bird and a fish
d) a crocodile is related to a lizard but is not related to a bird
And another example . . .
gibbon orangutan gorilla
chimp
human
x
3. Referring to the tree above, which is an accurate statement of
relationships?
a) a gibbon is more closely related to a orangutan than to a human
b) a gibbon is more closely related to a human than to a orangutan
c) a gibbon is equally related to a human and a orangutan
d) a gibbon is related to a orangutan but is not related to a human
How about this one . . . ?
mouse
termite
fungus
fern
sunflower
a
b
c
d
e
4. Which of the five nodes marked on the tree above corresponds to the
common ancestor(s) of a mouse and a fungus?
5. Which of the five nodes marked on the tree above corresponds to the
most recent common ancestor of a mouse and a fungus?
hornworts,
mosses, etc. Lepidodendron Equisetum
tree habit
ferns
gymnosperms angiosperms
loss of
leaves
seeds
secondary xylem (wood)
tree habit
true leaves
x
common ancestor
6. In the above example, assume the common ancestor of these plants was a herb
(herbaceous, i.e., not woody) and did not produce true leaves or seeds. Based on the
phylogeny and assuming that all evolutionary changes in these traits are shown, which of
the tips has a tree habit but lacks true leaves?
a) angiosperms
b) ferns
c) Equisetum
d) Lepidodendron
Blue tick marks identify lineages along which
e) hornworts, mosses, etc.
indicated trait changes have occurred
Consider the following evolutionary tree
or phylogeny . . .
fungus
“b” is correct. The most
recent common ancestor of
moss & a fern, node x, is more
recent in time (compared to
present) than the most recent
common ancestor of a moss &
a green alga, node y.
green
algae
moss
fern
conifer
x
y
1. Referring to the tree above, which is an accurate statement of
relationships?
a) a moss is more closely related to a green alga than to a fern
b) a moss is more closely related to a fern than to a green alga
c) a moss is equally related to a green alga and a fern
d) a moss is related to a green alga but is not related to a fern
Consider another example . . .
fish
Again, “b” is correct. The
most recent common ancestor
of a crocodile & a bird, node x,
is more recent in time
(compared to present) than
the most recent common
ancestor of a croc & a lizard,
node y.
lizard
crocodile dinosaur
bird
x
y
2a. Referring to the tree above, which is an accurate statement of
relationships?
a) a crocodile is more closely related to a lizard than to a bird
b) a crocodile is more closely related to a bird than to a lizard
c) a crocodile is equally related to a bird and a fish
d) a crocodile is related to a lizard but is not related to a bird
Does this help?
No, not really. “b” is the correct
answer. While a crocodile may
appear more “similar” to a lizard
in anatomy, morphology, ecology,
etc., the crocodile is more closely
related to a bird than to a lizard
based on recency of common
ancestry.
2b. Referring to the tree above, which is an accurate statement of
relationships?
a) a crocodile is more closely related to a lizard than to a bird
b) a crocodile is more closely related to a bird than to a lizard
c) a crocodile is equally related to a bird and a fish
d) a crocodile is related to a lizard but is not related to a bird
And another example . . .
gibbon orangutan gorilla
“c” is correct. Because the
gibbon shares the same most
recent common ancestor with
both an orangutan and a
human (node x), the gibbon is
“equally” related to both
chimp
human
x
3. Referring to the tree above, which is an accurate statement of
relationships?
a) a gibbon is more closely related to a orangutan than to a human
b) a gibbon is more closely related to a human than to a orangutan
c) a gibbon is equally related to a human and a orangutan
d) a gibbon is related to a orangutan but is not related to a human
How about this one . . . ?
mouse
termite
fungus
fern
sunflower
a
4. Nodes “c”, “d”, and
“e” are common
ancestors of the
mouse and fungus.
5. Node “c” is the most
recent common
ancestor of the mouse
and fungus.
b
c
d
e
4. Which of the five nodes marked on the tree above corresponds to the
common ancestor(s) of a mouse and a fungus?
5. Which of the five nodes marked on the tree above corresponds to the
most recent common ancestor of a mouse and a fungus?
hornworts,
mosses, etc. Lepidodendron Equisetum
“d”, Lepidodendron. The
change from herbaceous to
tree habit occurred along the
branch leading to this tip
taxon, while the change from
no leaves to true leaves
occurred after Lepidodendron
branched off from the rest of
the tip taxa.
tree habit
ferns
gymnosperms angiosperms
loss of
leaves
seeds
secondary xylem (wood)
tree habit
true leaves
x
common ancestor
6. In the above example, assume the common ancestor of these plants was a herb
(herbaceous, i.e., not woody) and did not produce true leaves or seeds. Based on the
phylogeny and assuming that all evolutionary changes in these traits are shown, which of
the tips has a tree habit but lacks true leaves?
a) angiosperms
b) ferns
c) Equisetum
d) Lepidodendron
Blue tick marks identify lineages along which
e) hornworts, mosses, etc.
indicated trait changes have occurred
How do we figure out the
evolutionary relationships among
organisms?
• We rely on shared, derived characters
– Shared = shared, found in multiple related
groups/species
– Derived = new, non-ancestral
– Characters = heritable traits of an organism
(e.g., morphology, physiology,
biochemistry, behavior, developmental
pattern, chromosome features, gene
sequences, etc.)
Homology, Analogy, and
Cladistics
• Homologies are characteristics that are
alike because of common descent
• Analogies, or homoplasies, are
characteristics that are alike in form or
function (probably due to similar selective
pressures), but do not share a common
ancestry (evolved independently). This is
known as convergence.
Cladistics
• A cladogram is a graphical representation of
the relatedness of species (their phylogeny)
based on the number of characteristics from
common ancestors that they share (can be
morphology, behavior, genes, etc.)
– One axis is time, with the top (or right) being the present
and the bottom (or left) being earlier.
– Nodes are the splitting points. Represent the most recent
common ancestor of two or more taxa.
• The more homologies, the more closely
related.
Parsimony
• Parsimony – the fewest number of evolutionary
changes is the most likely explanation. For
example, you don’t want to have feathers evolve
317 times in your phylogeny if you can help it.
The idea that feathers evolved only once is more
parsimonious.
• However, if you have a whole bunch of traits on
which to base your cladogram, it might be simpler
for one trait to evolve independently multiple
times. This trait is an analogy.
Monophyletic group
• A proper clade. Includes a common
ancestor and ALL descendants.
A
D
B
C
E
F
Paraphyletic Group
• Includes a common ancestor and only
SOME descendants. (e.g. great apes –
doesn’t include humans, others?)
A
D
B
C
E
F
Polyphyletic Group
• A group that share a common trait, but
the trait is an analogy (which means?)
e.g., birds of prey, marine mammals,
others?
A
D
B
C
E
F
Comparison
Clarification
• Ancestral/derived are terms that have to
be used relatively.
• For example, when comparing reptiles,
dinosaurs, birds, and mammals, body hair
is a derived feature for mammals.
However, when discussing mice, rats,
dogs, and people, body hair is ancestral
(the most recent common ancestor of all
four groups had body hair).
Evolution is…
• A change in gene
frequencies in a
population of
organisms over time.
 What causes this to happen?
Mechanisms of Evolution
• Mutations
•
Random changes in genetic material – generates variation in a
population
• Natural Selection
•
Process by which those more adapted to survive pass on more
genes
• Sexual Selection
•
Really a kind of natural selection. Process by which those more
adapted to successfully mate pass on more genes
• Gene flow
• Transfer of genes between 2 populations
• Genetic Drift (Founder Effect, Bottlenecking) – evolution
caused by random events, like a new geographic separation
or event that randomly kills individuals.
Natural
Selection
How do these small changes in gene
frequencies explain all the species on
earth today?
• It’s been a long time
• The Earth is ~4.5
BILLION yrs old
• 540 MILLION yrs ago
– 1st vertebrates
• 150 million years later,
1st vertebrates on land
• 200 million years later,
1st vertebrates in the
air!
Why do some organisms/ structures seem
perfect?
1. It has taken a long time,
and many, many
generations.
2. Look closer – there are a
lot of imperfections.
1. Vestigial organs
2. Imperfect “design”
3. The environment is
always changing.
4. Variation must be present
for selection to act upon.