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The evolution of complexity
A primer on evolution and
selection
1.Selection is on Phenotypes not genotypes
2. Most mutations are neutral because of the degeneracy of
genetic information. The wobble position of the 3rd codon often
leads to mutations that have no phenotype.
3. Evolution occurs on multiple (all) genes simultaneously – but at
different rates (tempos).
4. There is a potential for lateral gene transfer – especially in
prokaytotes.
5. Sexual recombination greatly increased genetic variability –
because genetic information is contained in discrete units
(genes) .
Molecular “clocks”
The basic Poisson function for a
mutation at any point in a codon
dN/dt (I) = e- kt (kt)I/ I !
The evolution of Eukaryotes
The acquisition of mitochondria and plasids –
driving forces and evolutionary consequences
Massive lateral gene transfers
Modes of Evolution
1. Horizontal versus lateral gene
transfer
2. Selection versus neutral
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Eukaryotes
Bacteria
Secondary symbionts
• The evolution of modern eukaryotic
phytoplankton
• Drivers for secondary symbiosis –
• retention of fixed N in the host cell
(extreme oligotrophy)
• plastid could obtain protection from
predation (armor)
Euglenophyta
Chlorophyta
Bacillariophyta
Chlorella
Odontella
ntcA
odpA
odpB
petJ
preA
rpl28
trpA
trpG
trxA
chlN
cpcA
cpcB
cpcG
dfr
glnB
gltB
hisH
infC
nblA
Nephroselmis
Cryptophyta
cemA
cpeB
ftrB
ilvB
ilvH
infB
minD
pbsA
psaK
rne
tsf
Euglena
ftsW
ndhA-I
ndhK
psaM
Guillardia
thiG
bas1
Cyanidium
pgmA
rpl9
rps1
syfB
syh
upp
Secondary endosymbiosis
clpP
ftsW
psbM
rbcLg
rpl22
accD
bas1
cpeB
infB
minD
pbsA
psbX
rps20
accA
accB
accD
apcA
apcB
apcD
apcE
apcF
argB
carA
Mesostigma
Porphyra
hisH
minD
ndhJ
odpB
rpl33
rps15
rps16
Glaucocystophyta
accD cysA
ccsA cysT
cemA ftsW
chlB infA
chlL minD
chlN ndhA-I
clpP ndhK
Secondary endosymbiosis
rps16
rpl21
Cyanophora
chlB
chlL
cpeA
dsbD
fabH
fdx
moeB
atpI rne
cemA rpl23
minD rpl32
odpB
cystA
cystT
infA
ndhA-K
rps15
> 90% of genes lost
Primary endosymbiosis
Ancestral
photosynthetic
prokaryote
bioY
crtE
groES
hemA
mntA
mntB
nadA
rbcSg
accA
accB
argB
bas1
carA
clpC
cpcG
cpeA
cpeB
dnaB
dfr
dsbD
fabH
fdx
ftrB
ftsH
glnB
gltB
ilvB
ilvH
infB
infC
moeB
nblA
ntcA
odpA
pbsA
petJ
pgmA
psaD
psaK
psaL
rbcLr
rbcSr
rpl4
rpl9
rpl13
rpl24
rpl27
rpl29
rpl31
rps1
secA
syfB
syh
thiG
trpA
trxA
tsf
upp
acpP
apcA
apcB
apcD
apcE
apcF
atpD
atpG
cpcA
cpcB
dnaK
groEL
hisH
petF
petM
preA
psaE
psaF
psbV
psbW
psbX
rbcR
rpl1
rpl3
rpl6
rpl11
rpl18
rpl28
rpl34
rpl35
rps5
rps6
rps10
rps13
rps17
rps20
secY
trpG
psbM
petA
petD
petL
psaI
rne
rpl19
rpoA
Marchantia
cysA, cysT
rpl21, ndhA-K
Pinus
cysA, cysT,
rpl21
chlB,L,N,
psaM
Nicotiana
acc
D
Oryza
chlI
ftsW
minD
odpB
rne
rpl5
rpl12
rpl19
rps9
tufA
Zea
Ancestral Rhodophyta genes?
minD
[minE]
ilvB (pbsA)
(cpeB) ilvH psaK
ftrB
(infB) tsf
Cryptophyta
Guillardia
[accD]
[odpB]
cemA
[(rne)]
Euglenophyta
Euglena
atpI
rpl23
rpl32
Bacillariophyta
Odontella
thiG
(bas1)
accA
accB
argB
carA
cpcG
(cpeA)
dfr
(dsbD)
(fabH)
(fdx)
glnB
gltB
infC
moeB
nblA
ntcA
odpA
petJ
(pgmA)
rpl9
(rps1)
Rhodophyta
(syfB)
(syh)
trpA
trxA
(upp)
cbbX
clpC
dnaB
ftsH
psaD
psaL
rbcSr
rpl4
rpl13
rpl24
rpl27
rpl29
rpl31
secA
acpA/P
atpD
atpG
dnaK
groEL
petF
petM
psaE
psaF
psbV
psbW
(psbX)
rbcR
apcA
apcB
apcD
apcE
rpl1
rpl3
rpl6
rpl11
rpl18
rpl21
rpl34
rpl35
rps5
rps6
rps10
rps13
rps17
(rps20)
secY
atpA
atpB
atpE
atpF
atpH
chlI
petB
petG
psaA
psaB
psaC
psaJ
[psaM]
psbA
psbB
ccsA
petA
petD
petL
psaI
rpl19
[rpl33]
[rps16]
rpoA
psbC
psbD
psbE
psbF
psbH
psbI
psbJ
psbK
psbL
psbN
psbT
rbcLg/r
rpl2
rpl5
rpl12
rpl14
rpl16
rpl20
[rpl22]
rpl36
rps2
rps3
rps4
rps7
rps8
rps9
rps11
rps12
rps14
rps18
rps19
rpoB
rpoC1
rpoC2
tufA
[rdpO]
cysA
cysT
infA
[I-CvuI]
[ndhA]
[ndhB]
[ndhC]
[ndhD]
[ndhE]
[ndhF]
[ndhG]
[ndhH]
[ndhI]
[ndhJ]
[ndhK]
[rps15]
chlB
(chlL)
chlN
apcF
cpcA preA
cpcB rpl28
(hisH) trpG
Glaucocystophyceae
Cyanophora
bioY
crte
groES
hemA
clpP
[ftsW]
psbM
mntA
mntB
nadA
rbcSg
Chlorophyta