Download Conditions of existence

developmental
mechanisms of
evolutionary
change
When Charles Darwin consulted his friend Thomas Huxley concerning
the origins of variation, Huxley told him that the differences between
organisms could be traced to differences in their development. He said
these differences “result not so much of the development of new parts
as of modification of parts already existing and common to both the
divergent types”.
This is a major tenet of evolutionary developmental biology also
known as “evo-devo” which views evolution as result of changes in
development.
If development is the change of gene expression and cell position over
time evolution is the change of development over time.
The two major views on the origin of species in the nineteenth century
1. Conditions of existence: This view championed by Georges Cuvier and Charles Bell focussed on
the differences between species that allowed each to adapt to its environment. Thus they
believed that the hand of the human, flipper of the seal and the wings of the birds and bats were
marvellous contrivances, each fashioned by the creator to adapt these animals to their
“conditions of existence”.
2. Unity of type: This view was championed by Etienne Geoffrey Saint-Hilaire and Richard Owen
was that “unity of type” (similarity of organisms, which Owens called “homologies”)is critical.
The hand of the human, flipper of the seal and the wings of the birds and bats were all
modifications of the same basic plan. In discovering the plan, one could find the form upon
which the creator designed these animals. The adaptations were secondary.
Darwin acknowledged his debt to these earlier debates when he wrote “ it is generally
acknowledged that all organic beings have been formed on two great laws-Unity of type and the
conditions of existence. Darwin went on to explain that his theory would explain unity of type by
descent from a common ancestor, while adaptations to the conditions of existence could be
explained by natural selection. Darwin called this concept descent with modification.
Preconditions of evolution: the developmental structure of the genome
 If natural selection can only operate on existing variants, where
does all the variation come from?
 If variation arose from changes in development then how could
development which is such a complex and fine tuned process
undergo changes without destroying the entire organism?
 Evolutionary developmental biologists showed that large
morphological changes could arise during development because of
two conditions that underlie development of all multicellular
organisms: modularity and molecular parsimony.
Modularity: Divergence through dissociation
Even early stages of development can be altered to produce evolutionary novelties
because development occurs through a series of discrete and interacting modules.
Examples of developmental modules are:
 Morphogenetic fields (heart, limb or eye)
 Signal transduction pathways (Wnt or BMP cascades)
 Imaginal discs
 Cell lineages (Inner cell mass or trophoblast)
 Insect parasegments
 Vertebrate organ rudiments.
The ability of one module to develop differently from the other is often called
dissociation.
An important discovery of evolutionary developmental biologists is that
there are not only anatomical units which are modular but DNA
regions that form enhancers are also modular.
This modularity of enhancers e.g. there can be multiple enhancers for
each gene allows particular sets of genes to be activated together as
well as allowing a particular gene to be expressed at different places.
Thus mutations that lead to loss or gain of a modular enhancer
element allows differential expression of genes possibly resulting in
adoption of different anatomical or physiological morphologies.
Duffy blood group substance
 Plasmodium vivax is one species of protozoan that causes malaria.
 Some African populations are immune to P. vivax because their RBCs lack the Duffy
glycoprotein that the P. vivax uses to attach to the RBC.
 Duffy glycoprotein is a receptor for IL8 and is found on cerebellar purkinje neurons,
blood veins and RBCs.
 The people immune to P. vivax express Duffy on Purkinje neurons and blood
vessels but not in the RBCs.
 A mutation in the RBC specific enhancer for Duffy has allowed these people to
retain expression of Duffy in other cells while losing it in the RBC.
 Thus the modular nature of the Duffy enhancer has made it possible for these
populations to be resistant to P. vivax infection.
Pitx1 and stickleback evolution
 There are two populations of threespine stickleback
fishes, one found in freshwater and the other is marine.
 Bony plates and pelvic spines characterize the marine
populations which serve as protection against predators.
 The freshwater population does not have the pelvic spines
because they do not have other fish preying on them
rather invertebrate predators could use the spines to
grasp on to them.
 By crossing spined varieties with spineless varieties and
using molecular markers to identify various regions of
chromosomes the major region which determines
development of pelvic spines was narrowed to distal end
of chromosome 7.
 Examining the candidate genes in this region known to be
expressed in the hindlimb then zeroed on to Pitx1.
 Found that the hindlimb specific enhancer of Pitx1 was
non-functional in the spineless variety.
 When this 2.5 kb DNA fragment from marine varieties was
fused to GFP and inserted into stickleback eggs, GFP was
expressed in the pelvis.
 Using this enhance to drive the expression of Pitx1 in
spineless varieties led them to develop spines.
Recruitment
 Often a new structure will form by recruitment
of existing modules (subroutines) into older
modules.
 The horns of dung beetles arose from cooption of leg patterning genes.
 The developmental network co-ordinating the
expression of Homothorax, Dachshund and
Distal-less in limb formation is used to
generate a novel structure, the horn in the
dung beetle larva.
 The placement of pigments on some
Drosophila wings arise when the enhancer for
the yellow locus (which makes black pigment)
becomes responsive to transcription factors
activated by Wingless.
Recruitment
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Beetles differ from other insects in forming an elytron---a forewing encased in a hard exoskeleton.
In beetles as in drosophila the Apterous gene is expressed in the dorsal compartment of the wing imaginal discs.
Apterous transcription factor organizes the tissue to differentiate dorsal wing structures.
However in beetles and no other known insects the Apterous also activates the exoskeleton genes in the
forewing while repressing them in the hindwing.
 Thus a new type of structure emerges from recruitment of one subroutine (exoskeleton development) into
another (dorsal forewing development).
Molecular parsimony: Gene duplication and divergence
The second precondition of macroevolution through developmental change
is molecular parsimony sometimes called the “small toolkit”.
Although development differs enormously from lineage to lineage,
development within all lineages use the same types of molecules.
The transcription factors, paracrine factors, cell adhesion molecules and
signal transduction cascades are remarkably similar between different phyla
It appear that jellyfish and flatworms use the same major kit of transcription
factors and paracrine factors as flies and vertebrates.
The small toolkit
 Certain transcription factors are (such as those of BMP, Hox and
Pax groups) are found in all animal phyla including cnidarians,
arthropods and chordates.
 The BMP levels appear to be used throughout the animal
kingdom to specifiy dorsal ventral axis. In sea anemone embryo
the Bmp4 and Dpp ortholog is expressed asymmetrically at the
edge of the blastopore (A).
 The Wnt and Hox genes are used to specify A-P axis throughout
all bilaterans. The Hox gene Anthox6 is expressed on the
blastopore side of the larval sea anemone (B).
 Pax6 appears to be involved in specifying light-sensing organs,
irrespective of whether it is an eye of a mollusc, insect or a
primate. Expression of mouse Pax6 in the fly leg can produce
an ectopic eye structures (C).
 Homologues of Otx2 specify head structures in both
invertebrates and vertebrates.
 Although insect and vertebrate hearts are very different both
are formed by using tinman/Nkx2.5
Duplication and divergence
One common thread that runs through
paracrine and transcription factor studies is
that genes that encode them come in
families.
How do these families come into existence?
The answer is through duplication of an
original gene and the subsequent mutation
of the original duplicates. This creates
families of genes that are related by common
descent (and often next to each other).
Subsequent mutations in the copies can
often lead to the subdivision of the gene’s
original function, such that each duplicated
gene is now expressed in a different cell
type.
The Hox genes were generated by successive rounds of gene duplication
Possible scheme for the formation of the
Hox paralogue clusters in metazoans by
gene duplication and divergence
The duplication and divergence of human SRGAP2
The SRGAP2 gene is found in a
single copy in genomes of all
mammals except humans.
In lineage giving rise to humans
duplications gave rise to four
similar versions of the gene,
designated A-D.
The SRGAP2A helps in
maturation of dendrites and
spine formation with some
help from SRGAP2B and D. It
acts by slowing down cell
proliferation and decreasing
the length and density of
dendritic processes.
The SRGAP2C is a partial
duplication and actually inhibits
spine formation thus delaying
the process of maturation
providing human brains with
greater flexibility.
Deep homology
In some instances homologous pathways made of
homologous components are used for the same function in
protostomes and deutrostomes. This has been called deep
homology.
The same set of instructions form the nervous system in
mice and flies.
In the fruit fly the TGFβ family member Dpp is expressed
dorsally and opposed by Sog ventrally.
In the mouse the TGFβ family member BMP4 is expressed
ventrally and countered by the Chordin dorsally.
The highest concentration of Chordin becomes the midline
which is dorsal in vertebrates and ventral in invertebrates
The concentration gradient of Bmp4/Dpp then specify the
regions of the nervous system in the same order Msh/Msx,
ind/Gsx and vnd/Nkx2.
Mechanisms of evolutionary change
In the 1940s, Richard Goldschmidt wrote that accumulation of small genetic changes was not sufficient to
generate evolutionarily novel structures such as neural crest, turtle shells or feathers. He argued that such
evolution could occur only though inheritable changes in genes that regulate development.
In 1977, this idea was extended by Francois Jacob. He said that evolution works with what it has by
combining existing parts in new ways rather than creating new parts. He further stated that such
“tinkering” would occur primarily in genes that construct the embryo, and not in genes that function in the
adult.
Wallace Arthur (2004) argued the following four ways in which this “tinkering” can occur at the level of
gene expression to generate phenotypic variation available for natural selection.
Heterotopy (change in location)
Heterochrony (change in time)
Heterometry (change in amount)
Heterotypy (change in kind)
Heterotopy (change in location)
The bat evolved its wings by changing the development of the
How the bat got its wings?
of the forelimb such that the cells in the interdigital webbing did
not die.
This very similar to how the duck retains webbing in the
hindlimb by blocking the BMPs that would otherwise cause the
interdigital cells to undergo apoptosis.
Both Gremlin and Fgf appear to block BMP functions in the bat
wing. Unlike other mammals bats express Fgf8 in their
interdigital mesenchyme. This also provides the mitotic signal
for digit extension in bats, thereby expanding the wing.
How the turtle got its shell?
 What distinguishes turtles from other
vertebrates are their ribs, which
migrate laterally into the dermis
instead of forming a rib cage.
 Certain regions of the turtle dermis
attract rib precursor cells and these
regions differ from that of other
vertebrates because they synthesize
Fgf10.
A and B: bright field and
autoradiographic staining for
Fgf10.
C: H&E staining of slightly later
turtle embryo showing rib
growing into dermis.
D: Hatchling turtle stained with
alizarin red to show bone.
Development of an Evolutionarily Novel Structure: Fibroblast Growth Factor Expression in
the Carapacial Ridge of Turtle Embryos
Loredo et al
JOURNAL OF GE.XAP. ELROIRMEEDNOT EATL AZLO.OLOGY (MOL DEV EVOL) 291:274–281 (2001)
 Once inside the dermis the rib cells
undergo endochondral ossification,
wherein cartilage cells are replaced
by bone and to do this they need
BMP.
 Since the ribs are embedded in the
dermis the dermal cells also respond
to the BMp and become bone.
How birds got their feathers?
 Although it was known that feathers were
modified reptilian scales, the mechanism of how
they formed has remained elusive. Harris and
colleagues have provided a developmental
mechanism for feather evolution.
 Stage 0 shows the expression of Shh and Bmp2 in
the scale bud where they are separated.
 Stage 1 represents a tubular feather as evolved
from an archosaurian scale. The Shh and Bmp
expressions are postulated to be at the tip.
 Stage 2 represents the evolution of a branched
feather evolved by further changing the expression
pattern of Shh and Bmp2 to form rows along the
proximo-distal axis. The interaction between Bmp2
and Shh proteins causes each of these regions to
form its own axis-the barbs of the feather
Shh-Bmp2 Signaling Module and the Evolutionary Origin and
Diversification of Feathers.
Harris et al
JOURNAL OF EXPERIMENTAL ZOOLOGY (MOL DEV EVOL) 294:160–176 (2002)
 In stage 3a changes in feather morphology evolved
by altering the pattern to produce a central rachis.
 Snakes evolved from four-limbed reptiles and
appear to have lost their legs in a two step
process.
 Paleontological and embryological evidence
suggest that snakes first lost their forelimbs
then their hind limbs. Fossil snakes have
found with no forelimbs but with hind limbs.
The most derived snakes such as vipers are
completely limbless while more primitive
snake such as boas and pythons have pelvic
girdles and rudimentary femurs.
 The missing limbs can be explained by altered
Hox gene expression. In most vertebrates the
forelimbs form just anterior to the most
anterior expression of Hoxc6. Caudal to this
point Hoxc6 in combination with HoxC8 helps
specify vertebrae to be thorasic and develop
 The loss of hindlimbs
ribs.
occur by a different
mechanism, hindlimb  During early python development Hoxc6 is
not expressed in absence of Hoxc8, so no
buds do begin to form
forelimbs develop. Rather there is continuous
but do not produce
expression of Hoxc6 and Hoxc8 telling the
anything more than a
femur due to lack of Shh vertebrae to form ribs throughout most of the
body.
expression and no AER.
How snakes lost their limbs?
Developmental basis of limblessness and
axial patterning in snakes
Martin J .Cohn*† & Cheryll Tickle†‡
NATURE |VOL 399 | 3 JUNE 1999
Heterochrony (change in time)
In heterochrony one module changes its time of expression or growth rate relative to other modules of the embryo
 Heterochrony is quite common in vertebrate evolution.
 In marsupials whose jaws and forelimbs develop at a
faster rate than those of placental mammals, allowing
the marsupial newborn to climb into the maternal pouch
and suckle.
 The enormous numbers of vertebrae and ribs formed in
snakes is due to heterochrony .
 The elongated fingers of the dolphin flipper appear to be
the result of heterochronic expression of Fgf8.
 Molecular heterochrony is observed in the lizard
Hemiergis which includes species with 3,4 or 5 digits per
limb. The number of digits is regulated by the length of
time Sonic hedgehog remains active in the limb bud’s
zone of polarizing activity. The shorter the duration of
Shh expression the fewer the number of digits.
 In primates there is a shift in the pattern of transcription
of a set of cerebral mRNAs such that the expression
pattern in the adult human resembles that in the
juvenile chimpanzee.
Heterometry
(change in amount)
 One of the best examples of
heterometry involves Darwin’s
finches, a set of closely related birds
on Galapagos islands.
Correlation between beak shape
and the expression of Bmp4 in
five species of Darwin’s finches
Correlation between beak length and the
amount of Calmodulin (CaM) gene
expression in six species of Darwin’s finches
 There are differences in beak
morphology between cactus finches
which have long narrow beaks,
helpful for probing cactus flowers and
ground finches with deep broad
beaks which help them to crack open
seeds.
 Abzhanov et al found a correlation
between beak shape and amount and
timing of Bmp4 expression.
 The same group also found through
microarray analysis that Calmodulin is
expressed fifteen fold higher in beaks
of cactus finches.
Role of BMP4 and Calmodulin (CaM) in beak evolution among Darwin’s finches
BMP4 and Calmodulin represent two targets of natural
selection, and together they explain the shape
variations of Darwin’s finches. BMP4 is regulated
heterochronically as well as heterometrically.
Calmodulin is regulated heterometrically. While natural
selection will allow certain morphologies to survive the
generation of these morphologies depend on
variations of developmentally regulatory genes such as
those for BMP4 and calmodulin.
Allometry
 Another consequence of modularity associated with
heterometry and heterochrony is allometry-changes which
occur when different parts of the organism grow at different
rates.
 As animals develop their shape changes , a result of differences
in timing and the duration of growth events.
 Indeed morphological evolution specially within a phylum is
due primarily to changes in body size and the relative sizes of
body parts. Such differential changes in growth rate can involve
altering a target cell’s sensitivity to growth factors or altering
the amounts of growth factors produced.
 A dramatic example of allometry comes from whale skulls. In
the very young (4-5 mm long) whale embryo the nose is in the
usual mammalian position. However the enormous growth of
the maxilla and premaxilla (upper jaw) pushes over the frontal
bone and forces the nose to the top of the skull.
Allometric growth in the whale head
 This new position of the nose turns it into blowhole, allowing
the whale to have a large and highly specialized jaw apparatus
and to breathe while swimming at the water’s surface.
Heterotypy (change in type)
In heterochrony, heterometry and heterotopy, mutations affect the regulatory region of the gene. The gene’s produc the
protein remains the same. The changes in heterotypy affect the coding regions of the gene.
How pregnancy may have evolved in mammals
Ability of the mammalian Hoxa11 protein, in combination with
Foxo1a, to promote expression of the uterine Prolactin enhancer
 One amazing feature of mammals is the female
uterus which can nurture and protect a
developing fetus within the mother’s body
 One of the key proteins enabling this is prolactin
as it promotes differentiation of uterine epithelial
cells, regulates trophoblast growth and
downregulates immune and inflammatory
responses.
 The mammalian Hoxa11 appears to have
undergone extensive mutation and selection in
the lineage giving rise to placental mammals such
that it now associates with Foxo1a. This
association allows the expression of prolactin
from a uterine specific enhancer.
 Hoxa11 from opossum and platypus and from
chicks does not upregulate prolactin.
Why insects have only six legs
Changes in Ubx protein associated with the insect clade in the evolution of arthropods
Of all arthropods only the insects have Ubx protein that is able to repress Distal-less expression and thereby inhibit
abdominal legs. This ability to repress Distal-less is due to a mutation whereby the original 3’end of the protein-coding
region was replaced by a group of nucelotides encoding a stretch of about 10 alanines. This polyalanine region
represses Distal-less expression in abdominal segments.