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EEB390: ALL lecture notes!

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Course
EEB 390

Institution
University Of Michigan - Ann Arbor

CUMULATIVE lecture notes for the class EEB390: Evolution at the University of Michigan. Notes were taken FA2023 under Prof. Stephen Smith.

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Uploaded on August 2, 2024
Number of pages 41
Written in 2023/2024
Type Class notes
Professor(s) Stephen smith
Contains Eeb390: evolution

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Natural
Selection
The
Components
of
Natural
Selection
●
Three
conditions
must
be
met
for
natural
selection
to
happen:
○
Variation:
individuals
must
differ
from
one
another
○
Inheritance:
differences
are
inherited
by
offspring
in
the
population
○
Differential
reproductive
success:
individuals
with
certain
traits
are
more
successful
at
surviving
and
reproducing
than
others
●
Mutation
is
one
of
the
major
sources
of
variation
○
Occur
at
random,
independently
of
whether
or
not
they
would
be
favored
●
When
biologists
study
nat
selection,
they
focus
on
how
a
specific
trait
of
interest
changes/remains
constant
over
time
●
Nat
selection
sorts
on
phenotypic
differences,
not
genotypes
○
Need
to
understand
how
genotype
and
environment
interplay
to
influence
phenotype
○
**
genes
code
for
traits
in
the
context
of
a
particular
set
of
environmental
conditions
**
■
Genes
themselves
do
not
code
for
traits
■
This
phenomenon
is
called
norm
of
reaction
■
Ex:
In
4
kinds
of
yarrow
plant,
genotype
1
grows
tallest
at
low
elevation,
but
genotype
4
grows
tallest
at
medium
elevation
EVEN
THO
THEIR
GENES
DON’T
CHANGE
Natural
Selection
and
Coat
Color
in
the
Oldfield
Mouse
(Example)
●
Studies
by
Hopi
Hoekstra
and
colleagues,
coat
color
in
the
oldfield
mouse
●
Hunted
by
visual
predators
such
as
owls
●
Usually
dark
in
coloration,
but
on
Santa
Rosa
Island
off
of
Florida,
they
are
much
lighter
●
Found
that
the
genotypes
of
the
two
mice
differently
expressed
two
genes
that
influence
fur
color
Phylogeny
●
Phylogeny:
shows
which
animals
are
closely
related
●
Parts
of
a
phylogenetic
tree:
○
Nodes:
hypothetical
ancestor
■
Denotes
speciation/seperation
event
○
Branch:
represents
evolution
of
a
lineage
○
Tip:
species,
individual,
other
entity
we
are
studying
■
Aka
Operational
Taxonomic
Unit
(OTU)
●
For
relatedness:
go
by
SHARED
HISTORY ○
More
shared
history
→
more
closely
related
(regardless
of
how
far
away
2
branches
are!)
●
Ancestral
Trait:
trait
in
ancestral
population/species
that
unless
lost
will
be
inherited
●
Derived
Trait:
trait
that
has
changed
state
from
the
ancestral
form
●
Homologous
Trait:
traits
found
in
a
set
of
species
bc
they
are
inherited
●
Analogous
Traits:
traits
found
in
a
set
of
species
but
not
because
of
shared
ancestry
(convergence)
○
Ex:
venomous
fish
have
evolved
at
least
3
times,
but
independently
of
each
other
●
Fun
vocab!
○
Synapomorphy:
shared
derived
trait
○
Homoplasy:
trait
shared
because
of
convergence
■
Ex:
flight
shared
w
birds
and
bees,
but
evolved
independently
○
Plesiomorphy:
ancestral
trait
○
Symplesiomorphy:
shared
ancestral
trait
●
Polytomy:
node
in
the
phylogeny
that
has
more
than
2
descendant
branches
○
Soft
polytomy:
caused
by
uncertainty
○
Hard
polytomy:
very
rapid
speciation
■
Simultaneous
speciation
●
Hybridization
can
complicate
phylogenies
but
don’t
worry
ab
it
:)
Rooting
●
Sometimes
display
trees
w
no
root
●
Showing
relationships
depends
where
root
is!
●
Ingroup:
subgroup
of
interest
in
a
study
●
Outgroup:
one
or
more
species
include
to
provide
direction
in
phylogenetic
study
●
Clade:
branch
of
a
tree
w
one
ancestor
and
ALL
its
descendants
●
When
looking
at
group
of
species,
look
at
most
recent
common
ancestor
(MRCA)
●
Monophyletic:
taxonomic
group
consisting
of
all
descendants
of
the
group’s
MRCA
(and
nothing
else) ●
●
Polyphyletic:
disjointed
group
of
descendants
(BAD)
○
Ex:
taxons
4,
5,
9,
and
10
●
Paraphyletic:
group
that
does
not
contain
all
the
descendants
of
the
group’s
most
common
ancestor
(BAD)
○
Ex:
taxons
6,
7,
1,
and
2
●
Sauropsida:
monophyletic
group
that
includes
all
birds
and
reptiles
(including
dinosaurs)
○
●
Vertebrates:
monophyletic
group
that
includes
fishes,
birds,
mammals,
etc
○
Fishes:
paraphyletic
group
that
doesn’t
include
tetrapods ●
Cladograms:
tree
with
no
info
in
branch
lengths
●
Phylogram:
tree
w
evolutionary
change
represented
as
branch
lengths
●
Chronogram:
tree
w
time
represented
as
branch
lengths
Genetic
Variation
Mendelian
Genetics
●
Law
of
segregation:
every
individual
has
2
gene
copies
at
a
locus,
these
copies
segregate
during
gamete
production
so
only
one
goes
into
a
gamete
○
Only
in
diploids
●
Locus:
physical
location
of
gene
on
chromosome
●
Gamete:
sex
cells
of
organism
●
Allele:
gene
variant
(R
and
r)
●
Law
of
independent
assortment:
allele
passed
for
one
trait
is
independent
of
allele
fro
another
trait
at
another
locus
for
a
gamete
○
Traits
are
randomly
passed
to
offspring
independently
○
Assumes
that
genes
are
unlinked
Genetics
Review!
●
Linkage
disequilibrium:
presence
of
statistical
association
between
allele
at
different
loci
○
Genes
on
same
chromosome
→
potential
that
they
tend
to
be
linked
●
Chromosomal
crossover
and
segregation
produces
gametes
help
produce
novel
allele
combos
in
offspring
○
Begins
link
b/n
geno
and
phenotype
○
Diff
traits
help
in
diff
environments
●
Transcription:
RNA
polymerase
reads
coding
sequence
of
DNA
→
produces
complementary
RNA
and
messenger
mRNA
●
Translation:
mRNA
decoded
by
ribosome
→
amino
acids
→
proteins
●
Codon:
three
nucleotides
(usually
→
amino
acid)
○
Stop
codons
end
translation,
start
codons
start
them
(AUG)
●
Redundancy
in
translation
–
diff
codons
make
same
amino
acid
○
Ex:
CUU,
CUC,
CUA,
and
CUG
all
code
for
Leucine
●
RNA
polymerase
binds
to
promoter
region,
signals
where
to
begin
transcription
●
Introns
not
encoded
into
proteins
but
can
serve
important
regulatory
functions
or
provide
spacing/secondary
structure
●
Exons
encoded
into
proteins

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