Evo........

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Evo........
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Evo........Devo
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Evo - Devo Evolution and Development I.
Background
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Evo - Devo I. Background - Embrologists have
long realized that organisms in different phyla
have different developmental "plans"
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Evo - Devo I. Background - Embrologists have
long realized that organisms in different phyla
have different developmental "plans" - And in a
phylum, there is the same developmental plan.
This is not necessarily what we might expect from
random mutation and evolution... why don't we see
as many differences in early developmental traits
as we see in later developing traits?
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- For instance, why do chordates have similar
development, even though cartilaginous fish and
other vertebrates are separated by 400 million
years of divergent evolution?
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Evo - Devo I. Background - Embrologists have
long realized that organisms in different phyla
have different developmental "plans" - And in a
phylum, there is the same developmental plan.
This is not necessarily what we might expect from
random mutation and evolution... why don't we see
as many differences in early developmental traits
as we see in later developing traits? - For
instance, why do chordates have similar
development, even though cartilaginous fish and
other vertebrates are separated by 400 million
years of divergent evolution. - Embryological
development is highly conserved, while
subsequently allowing extraordinary variation....
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Evo - Devo I. Background II. Core Processes -
Basic biological processes are CONSERVED, and the
enzymes that perform them are CONSERVED
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Evo - Devo I. Background II. Core Processes -
Basic biological processes are CONSERVED, and the
enzymes that perform them are CONSERVED DNA,
RNA, protein synthesis - ALL LIFE
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Evo - Devo I. Background II. Core Processes -
Basic biological processes are CONSERVED, and the
enzymes that perform them are CONSERVED DNA,
RNA, protein synthesis - ALL LIFE Membrane
structure and function - ALL EUK's
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Evo - Devo I. Background II. Core Processes -
Basic biological processes are CONSERVED, and the
enzymes that perform them are CONSERVED DNA,
RNA, protein synthesis - ALL LIFE Membrane
structure and function - ALL EUK's Cell junctions
- ALL METAZOA
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Evo - Devo I. Background II. Core Processes -
Basic biological processes are CONSERVED, and the
enzymes that perform them are CONSERVED DNA,
RNA, protein synthesis - ALL LIFE Membrane
structure and function - ALL EUK's Cell junctions
- ALL METAZOA Hox genes - ALL BILATERIA
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Evo - Devo I. Background II. Core Processes -
Basic biological processes are CONSERVED, and the
enzymes that perform them are CONSERVED DNA,
RNA, protein synthesis - ALL LIFE Membrane
structure and function - ALL EUK's Cell junctions
- ALL METAZOA Hox genes - ALL BILATERIA Limb
formation - ALL LAND VERTEBRATES
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Evo - Devo I. Background II. Core Processes -
Basic biological processes are CONSERVED, and the
enzymes that perform them are CONSERVED - Many
enzymes are more than 50 similar in AA sequence
in E. coli and H. sapiens, though separated by 2
billion years of divergence. - Of 548 metabolic
enzymes in E. coli, 50 are present in ALL LIFE,
and only 13 are unique to bacteria.
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Evo - Devo I. Background II. Core Processes -
Basic biological processes are CONSERVED, and the
enzymes that perform them are CONSERVED - Many
enzymes are more than 50 similar in AA sequence
in E. coli and H. sapiens. - Of 548 metabolic
enzymes in E. coli, 50 are present in ALL LIFE,
and only 13 are unique to bacteria. - So the
variation and diversity of life is NOT due to
changes in metabolic or structural genes... we
are all built out of the same stuff, that works
the same way at a cellular level.
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Evo - Devo I. Background II. Core Processes -
Basic biological processes are CONSERVED, and the
enzymes that perform them are CONSERVED - Many
enzymes are more than 50 similar in AA sequence
in E. coli and H. sapiens. - Of 548 metabolic
enzymes in E. coli, 50 are present in ALL LIFE,
and only 13 are unique to bacteria. - So the
variation and diversity of life is NOT due to
changes in metabolic or structural genes... we
are all built out of the same stuff, that works
the same way at a cellular level. - Variation is
largely due to HOW these processes are
REGULATED... 300 cell types in humans, all
descended from the zygote all genetically the
same.
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Development is NOT a
single process
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Development is NOT a
single process - Development is a well
choreographed dance of many parallel processes...
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Development is NOT a
single process - Development is a well
choreographed dance of many parallel
processes... - How is the parallelism
maintained, ESPECIALLY as one process evolves?
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Development is NOT a
single process - Development is a well
choreographed dance of many parallel
processes... - How is the parallelism
maintained, ESPECIALLY as one process evolves? -
Because they may be triggered by the same (or
subsets of the same) REGULATORS... these are
transcription factors that can turn suites of
metabolic/structural genes on and off.
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Development is NOT a
single process - Development is a well
choreographed dance of many parallel
processes... - How is the parallelism
maintained, ESPECIALLY as one process evolves? -
Because they may be triggered by the same (or
subsets of the same) REGULATORS... these are
transcription factors that can turn suites of
metabolic/structural genes on and off. And
transcription factors can interact.
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Best (and most
fundamental) examples are HOX genes. These are
'homeotic genes' that produce a variety of
transcription factors. The production and
localization of these transcription factors are
CRITICAL in determining the 'compartments' of
bilaterally symmetrical animals.
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Duplication of hox
genes can lead to differential regulation in
different segments, and different phenotypes in
different segments.
inhibition of limb development
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Duplication of hox
genes can lead to differential regulation in
different segments, and different phenotypes in
different segments. Each gene produces a DNA
binding protein that turns on a set of genes...
different hox genes produce different binding
proteins, that stimulate different sets of
genes...that are ALL regulated by THIS
transcription factor (linked regulation -
coordinated response).
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Effects can be
profound
antennaepedia
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Effects can be
profound - But they demonstrate the 'modularity'
of the developmental plan - only single units are
affected.
Bithorax
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Effects can be
profound - But they demonstrate the 'modularity'
of the developmental plan - only single units are
affected.
- 'Master Switches' that initiate downstream
cascades that can be very different... like
compound or vertebrate eyes.
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - and they are still
integrated with the rest of the organism For
example, the length of a breed's snout correlated
directly with the number of repeats in a gene
called Runx-2. Runx-2's tandem repeat consists of
two different three-base sequences, randomly
ordered along the length of the repeat. If
there's more of one threesome relative to the
other, that breed's muzzle tends to be longer and
straighter. Fonden and Garner. 2004. PNAS
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This protein is a member of the RUNX family of
transcription factors and has a Runt DNA-binding
domain. It is essential for osteoblastic
differentiation and skeletal morphogenesis and
acts as a scaffold for nucleic acids and
regulatory factors involved in skeletal gene
expression. The protein can bind DNA both as a
monomer or, with more affinity, as a subunit of a
heterodimeric complex. Transcript variants of the
gene that encode different protein isoforms
result from the use of alternate promoters as
well as alternate splicing.1 One gene of
interest may be RUNX2 (CBFA1). It is the only
gene in the genome known to cause cleidocranial
dysplasia, which is characterized by delayed
closure of cranial sutures, hypoplastic or
aplastic clavicles, a bell-shaped rib cage, and
dental abnormalities (70). Some of these features
affect morphological traits for which modern
humans differ from Neandertals as well as other
earlier hominins. For example, the cranial
malformations seen in cleidocranial dysplasia
include frontal bossing, i.e., a protruding
frontal bone. A more prominent frontal bone is a
feature that differs between modern humans and
Neandertals as well as other archaic hominins.
The clavicle, which is affected in cleidocranial
dysplasia, differs in morphology between modern
humans and Neandertals (71) and is associated
with a different architecture of the shoulder
joint. Finally, a bell-shaped rib cage is typical
of Neandertals and other archaic hominins. A
reasonable hypothesis is thus that an
evolutionary change in RUNX2 was of importance in
the origin of modern humans and that this change
affected aspects of the morphology of the upper
body and cranium.
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Types of Regulation
Enhancer - upstream activation sequence. Binding
site for transcription factor. Mutation here is
cis-regulation (within the operational "cistron")
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Types of Regulation
mutation in the transcription factor gene is
called trans-regulation
Enhancer - upstream activation sequence. Binding
site for transcription factor. Mutation here is
cis-regulation (within the operational "cistron")
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - Types of Regulation
mutation in the transcription factor gene is
called trans-regulation
Enhancer - upstream activation sequence. Binding
site for transcription factor. Mutation here is
cis-regulation (within the operational "cistron")
Each type modulates activity about 50 of the
time...
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - NOVELTY
Mutations may make an enhancer available to a
different transcription factor... and now that
gene is 'on' in a new tissue and can be used for
a new function. Crystallins are heat-shock
proteins and mitochondrial enzymes but when they
are expressed in the eye, they are used as
transparent structural proteins in a completely
different process.
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And of course, how they are arranged in lenses
vary.
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - NOVELTY
OR, an entirely new binding site can evolve -
they are typically quite short (6-10 bases) so
they will arise frequently by random
mutation...selection can then favor new
regulatory pathways.... KEEP THE OLD, but GAIN
NEW (sound familiar???)
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- Prud'homme et al. 2006. Repeated morphological
evolution through cis-regulatory changes in a
pleiotropic gene Nature 4401050-1053.
ac, The wing spots on male flies of the
Drosophila genus. Drosophila tristis (a) and D.
elegans (b) have wing spots that have arisen
during convergent evolution. Drosophila
gunungcola (c) instead evolved from a spotted
ancestor. d, Males wave their wings to display
the spots during elaborate courtship dances.
(Photographs courtesy of B. Prud'homme and S.
Carroll.)
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- Prud'homme et al. 2006. Repeated morphological
evolution through cis-regulatory changes in a
pleiotropic gene Nature 4401050-1053.
yellow gene
enzyme for pigment production
"spotted wing"
In their previous research, they found that
spotted members of both spotted clades had same
cis regulatory element (CRE). So, they
hypothesized that all members of the clade were
descended from a spotted ancestor (99 chance
ancestor was spotted - fig.)
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- Prud'homme et al. 2006. Repeated morphological
evolution through cis-regulatory changes in a
pleiotropic gene Nature 4401050-1053.
yellow gene
LOSS of the spot within this clade (an example of
convergent evolution AND reversion) occurred by
different mutations in same CRE.
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- Prud'homme et al. 2006. Repeated morphological
evolution through cis-regulatory changes in a
pleiotropic gene Nature 4401050-1053.
yellow gene
LOSS of the spot within this clade (an example of
convergent evolution AND reversion) occurred by
different mutations in same CRE. Importantly,
yellow is still on elsewhere. This is a
pleiotropic gene that has many effects.
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- Prud'homme et al. 2006. Repeated morphological
evolution through cis-regulatory changes in a
pleiotropic gene Nature 4401050-1053.
yellow gene
LOSS of the spot within this clade (an example of
convergent evolution AND reversion) occurred by
different mutations in same CRE. Importantly,
yellow is still on elsewhere. This is a
pleiotropic gene that has many effects. Shutting
it "off" by a mutation in the gene would cripple
it's activity throughout the organism. Here,
through cis regulation, it's expression is
modulated in only one tissue (wing).
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- Prud'homme et al. 2006. Repeated morphological
evolution through cis-regulatory changes in a
pleiotropic gene Nature 4401050-1053.
yellow gene
spotted wing
In D. tristis, the yellow gene is enhanced by a
completely different, independently evolved CRE.
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- Prud'homme et al. 2006. Repeated morphological
evolution through cis-regulatory changes in a
pleiotropic gene Nature 4401050-1053.
Two gains and two losses are due to independent
changes in the regulation of the yellow gene. The
developmental 'scaffold' for forming spots
exists... subsequent evolution of enhancement can
form a new anatomical trait, which can be rapidly
selected for by sexual selection.
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation - HETEROCHRONY -
paedomorphism - peramorphism - allometry All
simply changes in the developmental rates of
different structures or processes.
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Allometry in horn length relative to body size in
Beetles
Scarabaeidae Onthophagus
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Evolution of legs from fins
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Evolution of legs from fins
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory Behavior

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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory Behavior
- environmental cues affect cell activity -
production of growth factors
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory Behavior
- environmental cues affect cell activity -
production of growth factors - hypoxia -
stimulates cell to produce endothelial growth
factor
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory Behavior
- environmental cues affect cell activity -
production of growth factors - hypoxia -
stimulates cell to produce endothelial growth
factor - neighboring vascular tissue grows
towards the source of growth factor
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory Behavior
- environmental cues affect cell activity -
production of growth factors - hypoxia -
stimulates cell to produce endothelial growth
factor - neighboring vascular tissue grows
towards the source of growth factor - and
BINGO... now you have vascular tissue and hypoxia
is corrected
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory Behavior
- environmental cues affect cell activity -
production of growth factors - hypoxia -
stimulates cell to produce endothelial growth
factor - neighboring vascular tissue grows
towards the source of growth factor - and
BINGO... now you have vascular tissue and hypoxia
is corrected - Nerves and vessels grow in
response to local signals... the pattern is not
hardwired.
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory Behavior
- environmental cues affect cell activity -
production of growth factors - hypoxia -
stimulates cell to produce endothelial growth
factor - neighboring vascular tissue grows
towards the source of growth factor - and
BINGO... now you have vascular tissue and hypoxia
is corrected - Nerves and vessels grow in
response to local signals... the pattern is not
hardwired. - So, if bone growth changes,
muscles cell growth responds, and correct
ennervation and vascularization occurs on this
new platform.
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory
Behavior V. Physiology and Evolution
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stress response phenotype
Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory
Behavior V. Physiology and Evolution - stress
can reveal new phenotypes - "norm of reaction"
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stress response phenotype
Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory
Behavior V. Physiology and Evolution - stress
can reveal new phenotypes - "norm of reaction"
- (cloned plants raised in different environments
will look different, as a result of different
physiological responses and gene action.)
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stress response phenotype
Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory
Behavior V. Physiology and Evolution - stress
can reveal new phenotypes - "norm of reaction"
- (cloned plants raised in different environments
will look different, as a result of different
physiological responses and gene action.) -
Initially, this response is phenotypic and
probably suboptimal in integration. However,
mutations that stabilize this phenotype (create
it with greater integration) would be selected
for (If more integration means greater energetic
efficiency at achieving that phenotype, and more
energy to divert to reproduction).
selection
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stress response phenotype
Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory
Behavior V. Physiology and Evolution - stress
can reveal new phenotypes - "norm of reaction"
- (cloned plants raised in different environments
will look different, as a result of different
physiological responses and gene action.) -
Initially, this response is phenotypic and
probably suboptimal in integration. However,
mutations that stabilize this phenotype (create
it with greater integration) would be selected
for (If more integration means greater energetic
efficiency at achieving that phenotype, and more
energy to divert to reproduction). - So the
phenotype might not change, but it shifts from a
physiological stress response to a genetically
encoded norm. Subsequent stress expresses new
variation...
initially an inefficient phenotypic stress
response now an efficient and genetically
hardwired response.
selection
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory
Behavior V. Physiology and Evolution VI. The Role
of Physiology and Development in Evolution
Sources of Variation
Agents of Change
Mutation Recombination
Selection Drift Mutation Migration Non-Random
Mating
VARIATION
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory
Behavior V. Physiology and Evolution VI. The Role
of Physiology and Development in Evolution
Sources of Variation
Agents of Change
Selection Drift Mutation Migration Non-Random
Mating
Mutation Recombination
PHYSIOLOGY DEVELOPMENT
VARIATION
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Evo - Devo I. Background II. Core Processes III.
Weak Linkage Regulation IV. Exploratory
Behavior V. Physiology and Evolution VI. The Role
of Physiology and Development in Evolution VII.
Example - Darwin's Finches
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VII. Example - Darwin's Finches - two genes
interact in a co-ordinated way to determine beak
dimensions (Abzhanov et al. 2006. Nature
442563-567).
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VII. Example - Darwin's Finches - two genes
interact in a co-ordinated way to determine beak
dimensions (Abzhanov et al. 2006. Nature
442563-567). - BMP4 i a highly conserved
signaling molecule in all metazoa it is "bone
morphogen protein" that stimulates collegen
production and subsequent production of cartilage
and bone.
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VII. Example - Darwin's Finches - two genes
interact in a co-ordinated way to determine beak
dimensions (Abzhanov et al. 2006. Nature
442563-567). - BMP4 i a highly conserved
signaling molecule in all metazoa it is "bone
morphogen protein" that stimulates collegen
production and subsequent production of cartilage
and bone. - The timing and amount of BMP4 varies
during development of finches
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VII. Example - Darwin's Finches - two genes
interact in a co-ordinated way to determine beak
dimensions (Abzhanov et al. 2006. Nature
442563-567). - BMP4 i a highly conserved
signaling molecule in all metazoa it is "bone
morphogen protein" that stimulates collegen
production and subsequent production of cartilage
and bone. - The timing and amount of BMP4 varies
during development of finches - Large Ground
Finch produces more, and produces it earlier,
than other species.
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VII. Example - Darwin's Finches - two genes
interact in a co-ordinated way to determine beak
dimensions (Abzhanov et al. 2006. Nature
442563-567). - BMP4 i a highly conserved
signaling molecule in all metazoa it is "bone
morphogen protein" that stimulates collegen
production and subsequent production of cartilage
and bone. - The timing and amount of BMP4 varies
during development of finches - Large Ground
Finch produces more, and produces it earlier,
than other species. - And a second, Calmodulin,
is expressed more in long pointed beaks. CaM
modulates calcium signalling in cells
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VII. Example - Darwin's Finches - two genes
interact in a co-ordinated way to determine beak
dimensions (Abzhanov et al. 2006. Nature
442563-567).
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VII. Example - Darwin's Finches - two genes
interact in a co-ordinated way to determine beak
dimensions (Abzhanov et al. 2006. Nature
442563-567).
Used a virus to insert an up regulator of CaM
into the beak of growing chick embryos. This is a
kinase that increases absorption of CaM. Caused
beak elongation.
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VII. Example - Darwin's Finches - so, if you
remember, allometry like this is a common source
of adaptive variation that may often be involved
in adaptive radiations. - This variation is in
the developmental timing of action of the same
structural genes.